#new_packages

2016-12-12

Sean Davis (09:41:56): > @Sean Davis has joined the channel

Sean Davis (09:41:56): > set the channel description: RSS feed of new packages

Marcel Ramos Pérez (09:43:20): > @Marcel Ramos Pérez has joined the channel

Levi Waldron (09:43:20): > @Levi Waldron has joined the channel

Phil Chapman (09:43:20): > @Phil Chapman has joined the channel

Peter Hickey (09:43:20): > @Peter Hickey has joined the channel

Kasper D. Hansen (09:43:20): > @Kasper D. Hansen has joined the channel

Vince Carey (09:43:20): > @Vince Carey has joined the channel

Michael Lawrence (09:43:20): > @Michael Lawrence has joined the channel

Aedin Culhane (09:43:20): > @Aedin Culhane has joined the channel

Tim Triche (09:43:20): > @Tim Triche has joined the channel

Jack Zhu (09:43:21): > @Jack Zhu has joined the channel

Martin Morgan (09:43:21): > @Martin Morgan has joined the channel

Benjamin Haibe-Kains (09:43:21): > @Benjamin Haibe-Kains has joined the channel

Lucas Schiffer (09:43:21): > @Lucas Schiffer has joined the channel

Nitesh Turaga (09:43:21): > @Nitesh Turaga has joined the channel

New Packages: Bioconductor (15:56:25): > http://bioconductor.org/packages/MetaboSignal/ MetaboSignal MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathwaysMetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.link - Attachment (Bioconductor): MetaboSignal > MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.

2016-12-13

New Packages: Bioconductor (00:52:03): > http://bioconductor.org/packages/PharmacoGx/ PharmacoGx Analysis of Large-Scale Pharmacogenomic DataContains a set of functions to perform large-scale analysis of pharmacogenomic data.link - Attachment (Bioconductor): PharmacoGx > Contains a set of functions to perform large-scale analysis of pharmacogenomic data.

Benjamin Haibe-Kains (09:07:21): > Awesome package, really …

New Packages: Bioconductor (15:52:04): > http://bioconductor.org/packages/PathoStat/ PathoStat PathoStat Statistical Microbiome Analysis PackageThe purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis. > <a…

New Packages: Bioconductor (21:01:27): > http://bioconductor.org/packages/MetaboSignal/ MetaboSignal MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathwaysMetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.link - Attachment (Bioconductor): MetaboSignal > MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.

2016-12-14

New Packages: Bioconductor (11:01:25): > http://bioconductor.org/packages/alpine/ alpine alpineFragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.link - Attachment (Bioconductor): alpine > Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.

New Packages: Bioconductor (11:01:25): > http://bioconductor.org/packages/MetaboSignal/ MetaboSignal MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathwaysMetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.link - Attachment (Bioconductor): MetaboSignal > MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.

New Packages: Bioconductor (15:51:26): > http://bioconductor.org/packages/yamss/ yamss Tools for high-throughput metabolomicsTools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.link - Attachment (Bioconductor): yamss > Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.

New Packages: Bioconductor (15:51:26): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY. > <a…

2016-12-15

New Packages: Bioconductor (10:51:24): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (10:51:24): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically…

New Packages: Bioconductor (21:01:19): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically…

2016-12-16

New Packages: Bioconductor (02:52:05): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically…

New Packages: Bioconductor (10:47:08): > http://bioconductor.org/packages/Pi/ Pi Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network LevelPriority index or Pi is developed as a genomic-led target prioritisation system, with the focus on leveraging human genetic data to prioritise potential drug targets at the gene, pathway and network level. The long term goal is to use such information to enhance early-stage target validation. Based on evidence of disease association from genome-wide association studies (GWAS), this prioritisation system is able to generate evidence to support identification of…

New Packages: Bioconductor (15:52:01): > http://bioconductor.org/packages/psichomics/ psichomics Graphical Interface for Alternative Splicing Quantification, Analysis and VisualisationPackage with a Shiny-based graphical interface for the integrated analysis of alternative splicing data from The Cancer Genome Atlas (TCGA). This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA samples.link - Attachment (Bioconductor): psichomics > Package with a Shiny-based graphical interface for the integrated analysis of alternative splicing data from The Cancer Genome Atlas (TCGA). This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA samples.

2016-12-17

New Packages: Bioconductor (15:51:28): > http://bioconductor.org/packages/gcapc/ gcapc GC Aware Peak CallerPeak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated using generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.link - Attachment (Bioconductor): gcapc (development version) > Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated using generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.

2016-12-19

New Packages: Bioconductor (06:01:27): > http://bioconductor.org/packages/fCCAC/ fCCAC functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasetsAn application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq).link - Attachment (Bioconductor): fCCAC > An application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq).

New Packages: Bioconductor (15:46:26): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY. > <a…

New Packages: Bioconductor (20:52:16): > http://bioconductor.org/packages/scDD/ scDD Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributionsThis package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions. > <a…

2016-12-20

New Packages: Bioconductor (10:47:06): > http://bioconductor.org/packages/Pi/ Pi Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network LevelPriority index or Pi is developed as a genomic-led target prioritisation system, with the focus on leveraging human genetic data to prioritise potential drug targets at the gene, pathway and network level. The long term goal is to use such information to enhance early-stage target validation. Based on evidence of disease association from genome-wide association studies (GWAS), this prioritisation system is able to generate evidence to support identification of…

New Packages: Bioconductor (15:45:33): > http://bioconductor.org/packages/alpine/ alpine alpineFragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.link - Attachment (Bioconductor): alpine > Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.

2016-12-21

New Packages: Bioconductor (10:56:25): > http://bioconductor.org/packages/Pi/ Pi Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network LevelPriority index or Pi is developed as a genomic-led target prioritisation system, with the focus on leveraging human genetic data to prioritise potential drug targets at the gene, pathway and network level. The long term goal is to use such information to enhance early-stage target validation. Based on evidence of disease association from genome-wide association studies (GWAS), this prioritisation system is able to generate evidence to support identification of…

New Packages: Bioconductor (16:21:25): > http://bioconductor.org/packages/HelloRanges/ HelloRanges Introduce *Ranges to bedtools usersTranslates bedtools command-line invocations to R code calling functions from the Bioconductor Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.link - Attachment (Bioconductor): HelloRanges > Translates bedtools command-line invocations to R code calling functions from the Bioconductor Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.

New Packages: Bioconductor (21:01:31): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically…

2016-12-22

New Packages: Bioconductor (15:46:41): > http://bioconductor.org/packages/Pi/ Pi Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network LevelPriority index or Pi is developed as a genomic-led target prioritisation system, with the focus on leveraging human genetic data to prioritise potential drug targets at the gene, pathway and network level. The long term goal is to use such information to enhance early-stage target validation. Based on evidence of disease association from genome-wide association studies (GWAS), this prioritisation system is able to generate evidence to support identification of…

2016-12-25

New Packages: Bioconductor (15:51:25): > http://bioconductor.org/packages/RCAS/ RCAS RNA Centric Annotation SystemRCAS is an automated system that provides dynamic genome annotations for custom input files that contain transcriptomic regions. Such transcriptomic regions could be, for instance, peak regions detected by CLIP-Seq analysis that detect protein-RNA interactions, RNA modifications (alias the epitranscriptome), CAGE-tag locations, or any other collection of target regions at the level of the transcriptome. RCAS is designed as a reporting tool for the functional analysis of…

2016-12-29

New Packages: Bioconductor (05:56:24): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with…

New Packages: Bioconductor (20:56:24): > http://bioconductor.org/packages/CytoML/ CytoML GatingML interface for openCytoThis package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.link - Attachment (Bioconductor): CytoML > This package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.

2016-12-30

New Packages: Bioconductor (01:01:25): > http://bioconductor.org/packages/treeio/ treeio Base Classes and Functions for Phylogenetic Tree Input and OutputBase classes and functions for parsing and exporting phylogenetic trees.link - Attachment (Bioconductor): treeio (development version) > Base classes and functions for parsing and exporting phylogenetic trees.

2017-01-01

New Packages: Bioconductor (16:01:23): > http://bioconductor.org/packages/MetaboSignal/ MetaboSignal MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathwaysMetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.link - Attachment (Bioconductor): MetaboSignal > MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.

2017-01-02

New Packages: Bioconductor (15:51:23): > http://bioconductor.org/packages/DeepBlueR/ DeepBlueR DeepBlueRAccessing the DeepBlue Epigenetics Data Server through R.link - Attachment (Bioconductor): DeepBlueR > Accessing the DeepBlue Epigenetics Data Server through R.

2017-01-03

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/DeepBlueR/ DeepBlueR DeepBlueRAccessing the DeepBlue Epigenetics Data Server through R.link - Attachment (Bioconductor): DeepBlueR > Accessing the DeepBlue Epigenetics Data Server through R.

New Packages: Bioconductor (15:51:21): > http://bioconductor.org/packages/DeepBlueR/ DeepBlueR DeepBlueRAccessing the DeepBlue Epigenetics Data Server through R.link - Attachment (Bioconductor): DeepBlueR > Accessing the DeepBlue Epigenetics Data Server through R.

2017-01-04

New Packages: Bioconductor (00:56:23): > http://bioconductor.org/packages/treeio/ treeio Base Classes and Functions for Phylogenetic Tree Input and OutputBase classes and functions for parsing and exporting phylogenetic trees.link - Attachment (Bioconductor): treeio (development version) > Base classes and functions for parsing and exporting phylogenetic trees.

New Packages: Bioconductor (05:51:22): > http://bioconductor.org/packages/proFIA/ proFIA Preprocessing of FIA-HRMS dataFlow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including…

New Packages: Bioconductor (10:51:22): > http://bioconductor.org/packages/DeepBlueR/ DeepBlueR DeepBlueRAccessing the DeepBlue Epigenetics Data Server through R.link - Attachment (Bioconductor): DeepBlueR > Accessing the DeepBlue Epigenetics Data Server through R.

New Packages: Bioconductor (16:01:20): > http://bioconductor.org/packages/CytoML/ CytoML GatingML interface for openCytoThis package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.link - Attachment (Bioconductor): CytoML > This package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.

New Packages: Bioconductor (16:01:20): > http://bioconductor.org/packages/recount/ recount Explore and download data from the recount projectExplore and download data from the recount project available athttps://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential…

New Packages: Bioconductor (20:56:23): > http://bioconductor.org/packages/CytoML/ CytoML GatingML interface for openCytoThis package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.link - Attachment (Bioconductor): CytoML > This package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.

New Packages: Bioconductor (20:56:23): > http://bioconductor.org/packages/DeepBlueR/ DeepBlueR DeepBlueRAccessing the DeepBlue Epigenetics Data Server through R.link - Attachment (Bioconductor): DeepBlueR > Accessing the DeepBlue Epigenetics Data Server through R.

2017-01-05

New Packages: Bioconductor (16:01:21): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.link - Attachment (Bioconductor): MWASTools (development version) > MWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.

2017-01-06

New Packages: Bioconductor (05:51:22): > http://bioconductor.org/packages/DeepBlueR/ DeepBlueR DeepBlueRAccessing the DeepBlue Epigenetics Data Server through R.link - Attachment (Bioconductor): DeepBlueR > Accessing the DeepBlue Epigenetics Data Server through R.

New Packages: Bioconductor (10:56:21): > http://bioconductor.org/packages/DeepBlueR/ DeepBlueR DeepBlueRAccessing the DeepBlue Epigenetics Data Server through R.link - Attachment (Bioconductor): DeepBlueR > Accessing the DeepBlue Epigenetics Data Server through R.

New Packages: Bioconductor (15:56:22): > http://bioconductor.org/packages/DeepBlueR/ DeepBlueR DeepBlueRAccessing the DeepBlue Epigenetics Data Server through R.link - Attachment (Bioconductor): DeepBlueR > Accessing the DeepBlue Epigenetics Data Server through R.

2017-01-07

New Packages: Bioconductor (15:46:24): > http://bioconductor.org/packages/psichomics/ psichomics Graphical Interface for Alternative Splicing Quantification, Analysis and VisualisationPackage with a Shiny-based graphical interface for the integrated analysis of alternative splicing data from The Cancer Genome Atlas (TCGA). This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA samples.link - Attachment (Bioconductor): psichomics > Package with a Shiny-based graphical interface for the integrated analysis of alternative splicing data from The Cancer Genome Atlas (TCGA). This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA samples.

2017-01-08

New Packages: Bioconductor (15:51:24): > http://bioconductor.org/packages/DeepBlueR/ DeepBlueR DeepBlueRAccessing the DeepBlue Epigenetics Data Server through R.link - Attachment (Bioconductor): DeepBlueR > Accessing the DeepBlue Epigenetics Data Server through R.

2017-01-09

New Packages: Bioconductor (10:56:21): > http://bioconductor.org/packages/bigmelon/ bigmelon Illumina methylation array analysis for large experimentsMethods for working with Illumina arrays using gdsfmt.link - Attachment (Bioconductor): bigmelon > Methods for working with Illumina arrays using gdsfmt.

New Packages: Bioconductor (10:56:21): > http://bioconductor.org/packages/Pi/ Pi Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network LevelPriority index or Pi is developed as a genomic-led target prioritisation system, with the focus on leveraging human genetic data to prioritise potential drug targets at the gene, pathway and network level. The long term goal is to use such information to enhance early-stage target validation. Based on evidence of disease association from genome-wide association studies (GWAS), this prioritisation system is able to generate evidence to support identification of the specific modulated genes…

New Packages: Bioconductor (15:51:21): > http://bioconductor.org/packages/CytoML/ CytoML GatingML interface for openCytoThis package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.link - Attachment (Bioconductor): CytoML > This package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.

2017-01-10

New Packages: Bioconductor (15:51:21): > http://bioconductor.org/packages/mimager/ mimager mimager: The Microarray ImagerEasily visualize and inspect microarrays for spatial artifacts.link - Attachment (Bioconductor): mimager (development version) > Easily visualize and inspect microarrays for spatial artifacts.

New Packages: Bioconductor (20:51:23): > http://bioconductor.org/packages/mimager/ mimager mimager: The Microarray ImagerEasily visualize and inspect microarrays for spatial artifacts.link - Attachment (Bioconductor): mimager (development version) > Easily visualize and inspect microarrays for spatial artifacts.

2017-01-11

New Packages: Bioconductor (00:51:24): > http://bioconductor.org/packages/SPLINTER/ SPLINTER Splice Interpreter Of TranscriptsSPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.link - Attachment (Bioconductor): SPLINTER > SPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.

New Packages: Bioconductor (15:46:26): > http://bioconductor.org/packages/bigmelon/ bigmelon Illumina methylation array analysis for large experimentsMethods for working with Illumina arrays using gdsfmt.link - Attachment (Bioconductor): bigmelon > Methods for working with Illumina arrays using gdsfmt.

New Packages: Bioconductor (20:51:22): > http://bioconductor.org/packages/mimager/ mimager mimager: The Microarray ImagerEasily visualize and inspect microarrays for spatial artifacts.link - Attachment (Bioconductor): mimager (development version) > Easily visualize and inspect microarrays for spatial artifacts.

2017-01-12

New Packages: Bioconductor (10:56:20): > http://bioconductor.org/packages/Pi/ Pi Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network LevelPriority index or Pi is developed as a genomic-led target prioritisation system, with the focus on leveraging human genetic data to prioritise potential drug targets at the gene, pathway and network level. The long term goal is to use such information to enhance early-stage target validation. Based on evidence of disease association from genome-wide association studies (GWAS), this prioritisation system is able to generate evidence to support identification of the specific modulated genes…

New Packages: Bioconductor (20:51:22): > http://bioconductor.org/packages/CytoML/ CytoML GatingML interface for openCytoThis package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.link - Attachment (Bioconductor): CytoML > This package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.

2017-01-13

New Packages: Bioconductor (15:56:21): > http://bioconductor.org/packages/CytoML/ CytoML GatingML interface for openCytoThis package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.link - Attachment (Bioconductor): CytoML > This package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.

2017-01-17

New Packages: Bioconductor (10:56:21): > http://bioconductor.org/packages/HelloRanges/ HelloRanges Introduce *Ranges to bedtools usersTranslates bedtools command-line invocations to R code calling functions from the Bioconductor Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.link - Attachment (Bioconductor): HelloRanges > Translates bedtools command-line invocations to R code calling functions from the Bioconductor Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.

New Packages: Bioconductor (10:56:21): > http://bioconductor.org/packages/StarBioTrek/ StarBioTrek StarBioTrekThis tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.link - Attachment (Bioconductor): StarBioTrek > This tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.

New Packages: Bioconductor (10:56:21): > http://bioconductor.org/packages/scDD/ scDD Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributionsThis package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.link - Attachment (Bioconductor): scDD (development version) > This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.

2017-01-19

New Packages: Bioconductor (10:56:21): > http://bioconductor.org/packages/methylKit/ methylKit DNA methylation analysis from high-throughput bisulfite sequencing resultsmethylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Perl is needed to read SAM files only.link - Attachment (Bioconductor): methylKit > methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Perl is needed to read SAM files only.

New Packages: Bioconductor (16:06:23): > http://bioconductor.org/packages/Pi/ Pi Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network LevelPriority index or Pi is developed as a genomic-led target prioritisation system, with the focus on leveraging human genetic data to prioritise potential drug targets at the gene, pathway and network level. The long term goal is to use such information to enhance early-stage target validation. Based on evidence of disease association from genome-wide association studies (GWAS), this prioritisation system is able to generate evidence to support identification of the specific modulated genes…

New Packages: Bioconductor (16:06:23): > http://bioconductor.org/packages/psichomics/ psichomics Graphical Interface for Alternative Splicing Quantification, Analysis and VisualisationPackage with a Shiny-based graphical interface for the integrated analysis of alternative splicing data from The Cancer Genome Atlas (TCGA). This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA samples.link - Attachment (Bioconductor): psichomics > Package with a Shiny-based graphical interface for the integrated analysis of alternative splicing data from The Cancer Genome Atlas (TCGA). This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA samples.

2017-01-20

New Packages: Bioconductor (00:56:24): > http://bioconductor.org/packages/statTarget/ statTarget Statistical Analysis of Metabolite ProfileAn easy to use tool provides a graphical user interface for quality control based shift signal correction, integration of metabolomic data from multi-batch experiments, and the comprehensive statistic analysis in non-targeted or targeted metabolomics.link - Attachment (Bioconductor): statTarget > An easy to use tool provides a graphical user interface for quality control based shift signal correction, integration of metabolomic data from multi-batch experiments, and the comprehensive statistic analysis in non-targeted or targeted metabolomics.

New Packages: Bioconductor (00:56:25): > http://bioconductor.org/packages/treeio/ treeio Base Classes and Functions for Phylogenetic Tree Input and OutputBase classes and functions for parsing and exporting phylogenetic trees.link - Attachment (Bioconductor): treeio (development version) > Base classes and functions for parsing and exporting phylogenetic trees.

New Packages: Bioconductor (10:46:22): > http://bioconductor.org/packages/clusterSeq/ clusterSeq Clustering of high-throughput sequencing data by identifying co-expression patternsIdentification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.link - Attachment (Bioconductor): clusterSeq (development version) > Identification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.

New Packages: Bioconductor (15:51:22): > http://bioconductor.org/packages/Pi/ Pi Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network LevelPriority index or Pi is developed as a genomic-led target prioritisation system, with the focus on leveraging human genetic data to prioritise potential drug targets at the gene, pathway and network level. The long term goal is to use such information to enhance early-stage target validation. Based on evidence of disease association from genome-wide association studies (GWAS), this prioritisation system is able to generate evidence to support identification of the specific modulated genes…

New Packages: Bioconductor (15:51:22): > http://bioconductor.org/packages/annotatr/ annotatr Annotation of Genomic Regions to Genomic AnnotationsGiven a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5’UTRs, exons, introns, and 3’UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic…

2017-01-22

New Packages: Bioconductor (10:51:23): > http://bioconductor.org/packages/psichomics/ psichomics Graphical Interface for Alternative Splicing Quantification, Analysis and VisualisationPackage with a Shiny-based graphical interface for the integrated analysis of alternative splicing data from The Cancer Genome Atlas (TCGA). This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA samples.link - Attachment (Bioconductor): psichomics > Package with a Shiny-based graphical interface for the integrated analysis of alternative splicing data from The Cancer Genome Atlas (TCGA). This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA samples.

New Packages: Bioconductor (15:46:24): > http://bioconductor.org/packages/bigmelon/ bigmelon Illumina methylation array analysis for large experimentsMethods for working with Illumina arrays using gdsfmt.link - Attachment (Bioconductor): bigmelon > Methods for working with Illumina arrays using gdsfmt.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/bigmelon/ bigmelon Illumina methylation array analysis for large experimentsMethods for working with Illumina arrays using gdsfmt.link - Attachment (Bioconductor): bigmelon > Methods for working with Illumina arrays using gdsfmt.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/splatter/ splatter Simple Simulation of Single-cell RNA Sequencing DataSplatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented.link - Attachment (Bioconductor): splatter (development version) > Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented.

2017-01-24

New Packages: Bioconductor (02:51:22): > http://bioconductor.org/packages/goSTAG/ goSTAG A tool to use GO Subtrees to Tag and Annotate Genes within a setGene lists derived from the results of genomic analyses are rich in biological information. For instance, differentially expressed genes (DEGs) from a microarray or RNA-Seq analysis are related functionally in terms of their response to a treatment or condition. Gene lists can vary in size, up to several thousand genes, depending on the robustness of the perturbations or how widely different the conditions are biologically. Having a way to associate biological relatedness between hundreds and…

New Packages: Bioconductor (05:56:22): > http://bioconductor.org/packages/SVAPLSseq/ SVAPLSseq SVAPLSseq-An R package to adjust for the hidden factors of variability in differential gene expression studies based on RNAseq dataThe package contains functions that are intended for the identification of differentially expressed genes between two groups of samples from RNAseq data after adjusting for various hidden biological and technical factors of variability.link - Attachment (Bioconductor): SVAPLSseq > The package contains functions that are intended for the identification of differentially expressed genes between two groups of samples from RNAseq data after adjusting for various hidden biological and technical factors of variability.

New Packages: Bioconductor (05:56:22): > http://bioconductor.org/packages/proFIA/ proFIA Preprocessing of FIA-HRMS dataFlow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and…

New Packages: Bioconductor (15:56:22): > http://bioconductor.org/packages/karyoploteR/ karyoploteR Karyotype plots with arbitrary datakaryoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.link - Attachment (Bioconductor): karyoploteR (development version) > karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

2017-01-25

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/MetaboSignal/ MetaboSignal MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathwaysMetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.link - Attachment (Bioconductor): MetaboSignal > MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.

New Packages: Bioconductor (10:51:22): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.link - Attachment (Bioconductor): MWASTools (development version) > MWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.

2017-01-26

New Packages: Bioconductor (10:51:22): > http://bioconductor.org/packages/MODA/ MODA MODA: MOdule Differential Analysis for weighted gene co-expression networkMODA can be used to estimate and construct condition-specific gene co-expression networks, and identify differentially expressed subnetworks as conserved or condition specific modules which are potentially associated with relevant biological processes.link - Attachment (Bioconductor): MODA > MODA can be used to estimate and construct condition-specific gene co-expression networks, and identify differentially expressed subnetworks as conserved or condition specific modules which are potentially associated with relevant biological processes.

2017-01-28

New Packages: Bioconductor (10:52:57): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.link - Attachment (Bioconductor): MWASTools (development version) > MWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.

New Packages: Bioconductor (10:52:57): > http://bioconductor.org/packages/sampleClassifier/ sampleClassifier Sample ClassifierThe package is designed to classify gene expression profiles.link - Attachment (Bioconductor): sampleClassifier (development version) > The package is designed to classify gene expression profiles.

New Packages: Bioconductor (10:52:57): > http://bioconductor.org/packages/geneClassifiers/ geneClassifiers Application of gene classifiersThis packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input.link - Attachment (Bioconductor): geneClassifiers (development version) > This packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input.

2017-01-29

New Packages: Bioconductor (06:36:25): > http://bioconductor.org/packages/REMP/ REMP Repetitive Element Methylation PredictionMachine learing-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE. > > <a…

New Packages: Bioconductor (15:56:24): > http://bioconductor.org/packages/REMP/ REMP Repetitive Element Methylation PredictionMachine learing-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE. > > <a…

2017-01-30

New Packages: Bioconductor (00:51:24): > http://bioconductor.org/packages/REMP/ REMP Repetitive Element Methylation PredictionMachine learing-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE. > > <a…

New Packages: Bioconductor (05:51:22): > http://bioconductor.org/packages/REMP/ REMP Repetitive Element Methylation PredictionMachine learing-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE. > > <a…

New Packages: Bioconductor (10:56:22): > http://bioconductor.org/packages/MODA/ MODA MODA: MOdule Differential Analysis for weighted gene co-expression networkMODA can be used to estimate and construct condition-specific gene co-expression networks, and identify differentially expressed subnetworks as conserved or condition specific modules which are potentially associated with relevant biological processes.link - Attachment (Bioconductor): MODA > MODA can be used to estimate and construct condition-specific gene co-expression networks, and identify differentially expressed subnetworks as conserved or condition specific modules which are potentially associated with relevant biological processes.

New Packages: Bioconductor (10:56:22): > http://bioconductor.org/packages/recount/ recount Explore and download data from the recount projectExplore and download data from the recount project available athttps://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression…

New Packages: Bioconductor (10:56:22): > http://bioconductor.org/packages/SVAPLSseq/ SVAPLSseq SVAPLSseq-An R package to adjust for the hidden factors of variability in differential gene expression studies based on RNAseq dataThe package contains functions that are intended for the identification of differentially expressed genes between two groups of samples from RNAseq data after adjusting for various hidden biological and technical factors of variability.link - Attachment (Bioconductor): SVAPLSseq > The package contains functions that are intended for the identification of differentially expressed genes between two groups of samples from RNAseq data after adjusting for various hidden biological and technical factors of variability.

New Packages: Bioconductor (10:56:22): > http://bioconductor.org/packages/fCCAC/ fCCAC functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasetsAn application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq).link - Attachment (Bioconductor): fCCAC > An application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq).

New Packages: Bioconductor (18:11:21): > http://bioconductor.org/packages/recount/ recount Explore and download data from the recount projectExplore and download data from the recount project available athttps://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression…

New Packages: Bioconductor (18:11:21): > http://bioconductor.org/packages/karyoploteR/ karyoploteR Karyotype plots with arbitrary datakaryoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.link - Attachment (Bioconductor): karyoploteR (development version) > karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

New Packages: Bioconductor (18:11:21): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version) > TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data.

2017-01-31

New Packages: Bioconductor (15:46:20): > http://bioconductor.org/packages/karyoploteR/ karyoploteR Karyotype plots with arbitrary datakaryoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.link - Attachment (Bioconductor): karyoploteR (development version) > karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

New Packages: Bioconductor (15:46:20): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version) > TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data.

2017-02-01

New Packages: Bioconductor (00:56:24): > http://bioconductor.org/packages/REMP/ REMP Repetitive Element Methylation PredictionMachine learing-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE. > > <a…

New Packages: Bioconductor (11:06:21): > http://bioconductor.org/packages/matter/ matter A framework for rapid prototyping with binary data on diskMemory-efficient reading, writing, and manipulation of structured binary data on disk as vectors, matrices, and arrays. This package is designed to be used as a back-end for Cardinal for working with high-resolution mass spectrometry imaging data.link - Attachment (Bioconductor): matter > Memory-efficient reading, writing, and manipulation of structured binary data on disk as vectors, matrices, and arrays. This package is designed to be used as a back-end for Cardinal for working with high-resolution mass spectrometry imaging data.

2017-02-02

New Packages: Bioconductor (00:51:24): > http://bioconductor.org/packages/splatter/ splatter Simple Simulation of Single-cell RNA Sequencing DataSplatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented.link - Attachment (Bioconductor): splatter (development version) > Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented.

2017-02-03

New Packages: Bioconductor (00:56:23): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (11:01:22): > http://bioconductor.org/packages/REMP/ REMP Repetitive Element Methylation PredictionMachine learing-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE. > > <a…

New Packages: Bioconductor (15:46:20): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version) > TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data.

2017-02-04

New Packages: Bioconductor (20:56:24): > http://bioconductor.org/packages/REMP/ REMP Repetitive Element Methylation PredictionMachine learing-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE. > > <a…

2017-02-05

New Packages: Bioconductor (00:56:24): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

2017-02-06

New Packages: Bioconductor (11:01:21): > http://bioconductor.org/packages/clusterSeq/ clusterSeq Clustering of high-throughput sequencing data by identifying co-expression patternsIdentification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.link - Attachment (Bioconductor): clusterSeq (development version) > Identification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.

New Packages: Bioconductor (20:46:23): > http://bioconductor.org/packages/annotatr/ annotatr Annotation of Genomic Regions to Genomic AnnotationsGiven a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5’UTRs, exons, introns, and 3’UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic…

2017-02-07

New Packages: Bioconductor (15:46:21): > http://bioconductor.org/packages/annotatr/ annotatr Annotation of Genomic Regions to Genomic AnnotationsGiven a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5’UTRs, exons, introns, and 3’UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic…

New Packages: Bioconductor (15:46:21): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (20:56:23): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

2017-02-08

New Packages: Bioconductor (05:51:22): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/annotatr/ annotatr Annotation of Genomic Regions to Genomic AnnotationsGiven a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5’UTRs, exons, introns, and 3’UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic…

New Packages: Bioconductor (21:01:21): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

2017-02-09

New Packages: Bioconductor (00:56:24): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (05:51:22): > http://bioconductor.org/packages/StarBioTrek/ StarBioTrek StarBioTrekThis tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.link - Attachment (Bioconductor): StarBioTrek > This tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.

New Packages: Bioconductor (12:16:22): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version) > TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data.

New Packages: Bioconductor (15:56:20): > http://bioconductor.org/packages/recount/ recount Explore and download data from the recount projectExplore and download data from the recount project available athttps://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression…

2017-02-12

New Packages: Bioconductor (16:01:24): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version) > TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data.

2017-02-13

New Packages: Bioconductor (00:51:22): > http://bioconductor.org/packages/meshes/ meshes MeSH Enrichment and Semantic analysesMeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide…

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/Pi/ Pi Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network LevelPriority index or Pi is developed as a genomic-led target prioritisation system, with the focus on leveraging human genetic data to prioritise potential drug targets at the gene, pathway and network level. The long term goal is to use such information to enhance early-stage target validation. Based on evidence of disease association from genome-wide association studies (GWAS), this prioritisation system is able to generate evidence to support identification of the specific modulated genes…

2017-02-14

New Packages: Bioconductor (05:56:21): > http://bioconductor.org/packages/SPLINTER/ SPLINTER Splice Interpreter Of TranscriptsSPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.link - Attachment (Bioconductor): SPLINTER > SPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.

New Packages: Bioconductor (20:51:24): > http://bioconductor.org/packages/recount/ recount Explore and download data from the recount projectExplore and download data from the recount project available athttps://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression…

2017-02-16

New Packages: Bioconductor (10:56:25): > http://bioconductor.org/packages/annotatr/ annotatr Annotation of Genomic Regions to Genomic AnnotationsGiven a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5’UTRs, exons, introns, and 3’UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic…

New Packages: Bioconductor (15:51:24): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (20:51:23): > http://bioconductor.org/packages/bigmelon/ bigmelon Illumina methylation array analysis for large experimentsMethods for working with Illumina arrays using gdsfmt.link - Attachment (Bioconductor): bigmelon > Methods for working with Illumina arrays using gdsfmt.

2017-02-17

New Packages: Bioconductor (05:51:25): > http://bioconductor.org/packages/SPLINTER/ SPLINTER Splice Interpreter Of TranscriptsSPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.link - Attachment (Bioconductor): SPLINTER > SPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.

New Packages: Bioconductor (10:51:23): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.link - Attachment (Bioconductor): MWASTools (development version) > MWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.

2017-02-18

New Packages: Bioconductor (20:51:27): > http://bioconductor.org/packages/psichomics/ psichomics Graphical Interface for Alternative Splicing Quantification, Analysis and VisualisationPackage with a Shiny-based graphical interface for the integrated analysis of alternative splicing data from The Cancer Genome Atlas (TCGA). This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA samples.link - Attachment (Bioconductor): psichomics > Package with a Shiny-based graphical interface for the integrated analysis of alternative splicing data from The Cancer Genome Atlas (TCGA). This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA samples.

2017-02-19

New Packages: Bioconductor (20:56:26): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version) > TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data.

2017-02-20

New Packages: Bioconductor (10:51:24): > http://bioconductor.org/packages/proFIA/ proFIA Preprocessing of FIA-HRMS dataFlow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and…

2017-02-21

New Packages: Bioconductor (05:46:24): > http://bioconductor.org/packages/ramwas/ ramwas Fast Methylome-Wide Association Study Pipeline for Enrichment PlatformsRaMWAS provides a complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association…

New Packages: Bioconductor (10:46:23): > http://bioconductor.org/packages/BiocWorkflowTools/ BiocWorkflowTools Tools to aid the development of Bioconductor Workflow packagesProvides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.link - Attachment (Bioconductor): BiocWorkflowTools > Provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.

New Packages: Bioconductor (15:56:22): > http://bioconductor.org/packages/KEGGlincs/ KEGGlincs Visualize all edges within a KEGG pathway and overlay LINCS data [option]See what is going on ‘under the hood’ of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.link - Attachment (Bioconductor): KEGGlincs > See what is going on ‘under the hood’ of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.

New Packages: Bioconductor (15:56:22): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version) > TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data.

New Packages: Bioconductor (15:56:22): > http://bioconductor.org/packages/Logolas/ Logolas Flexible and Customized Logo Plots using symbols, alphabets, numbers and alphanumeric stringsProduces logo plots of a variety of symbols and names comprising English alphabets, numerics and punctuations. Can be used for sequence motif generation, mutation pattern generation, protein amino acid geenration and symbol strength representation in any generic context.link - Attachment (Bioconductor): Logolas (development version) > Produces logo plots of a variety of symbols and names comprising English alphabets, numerics and punctuations. Can be used for sequence motif generation, mutation pattern generation, protein amino acid geenration and symbol strength representation in any generic context.

2017-02-22

New Packages: Bioconductor (00:51:26): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version) > TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data.

New Packages: Bioconductor (10:51:23): > http://bioconductor.org/packages/DMRScan/ DMRScan Detection of Differentially Methylated RegionsThis package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The scan statistic will depend on a sequence of window sizes (# of CpGs within each window) and on a threshold for each window size. This threshold can be calculated by three different means: i) analytically using Siegmundet.al(2012) solution (preferred), ii) an important sampling as suggested by Zhang (2008), and a…

New Packages: Bioconductor (15:51:24): > http://bioconductor.org/packages/MCbiclust/ MCbiclust Massive correlating biclusters for gene expression data and associated methodsCustom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.link - Attachment (Bioconductor): MCbiclust (development version) > Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

New Packages: Bioconductor (20:51:26): > http://bioconductor.org/packages/recount/ recount Explore and download data from the recount projectExplore and download data from the recount project available athttps://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression…

New Packages: Bioconductor (20:51:26): > http://bioconductor.org/packages/KEGGlincs/ KEGGlincs Visualize all edges within a KEGG pathway and overlay LINCS data [option]See what is going on ‘under the hood’ of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.link - Attachment (Bioconductor): KEGGlincs > See what is going on ‘under the hood’ of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.

New Packages: Bioconductor (20:51:26): > http://bioconductor.org/packages/yamss/ yamss Tools for high-throughput metabolomicsTools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.link - Attachment (Bioconductor): yamss > Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.

2017-02-23

New Packages: Bioconductor (10:46:23): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version) > TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data.

New Packages: Bioconductor (16:01:23): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version) > TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data.

2017-02-24

New Packages: Bioconductor (00:56:25): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (10:46:24): > http://bioconductor.org/packages/MCbiclust/ MCbiclust Massive correlating biclusters for gene expression data and associated methodsCustom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.link - Attachment (Bioconductor): MCbiclust (development version) > Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

2017-02-25

New Packages: Bioconductor (05:51:27): > http://bioconductor.org/packages/MetaboSignal/ MetaboSignal MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathwaysMetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.link - Attachment (Bioconductor): MetaboSignal > MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.

New Packages: Bioconductor (05:51:27): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.link - Attachment (Bioconductor): MWASTools (development version) > MWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.

New Packages: Bioconductor (10:51:27): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.link - Attachment (Bioconductor): MWASTools (development version) > MWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.

New Packages: Bioconductor (10:51:27): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version)

2017-02-26

New Packages: Bioconductor (05:46:27): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version)

New Packages: Bioconductor (20:51:25): > http://bioconductor.org/packages/yamss/ yamss Tools for high-throughput metabolomicsTools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.link - Attachment (Bioconductor): yamss > Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.

2017-02-27

New Packages: Bioconductor (15:52:00): > http://bioconductor.org/packages/recount/ recount Explore and download data from the recount projectExplore and download data from the recount project available athttps://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression…

New Packages: Bioconductor (15:52:00): > http://bioconductor.org/packages/KEGGlincs/ KEGGlincs Visualize all edges within a KEGG pathway and overlay LINCS data [option]See what is going on ‘under the hood’ of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.link - Attachment (Bioconductor): KEGGlincs > See what is going on ‘under the hood’ of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.

New Packages: Bioconductor (20:51:23): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version)

2017-02-28

New Packages: Bioconductor (00:51:27): > http://bioconductor.org/packages/annotatr/ annotatr Annotation of Genomic Regions to Genomic AnnotationsGiven a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5’UTRs, exons, introns, and 3’UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic…

New Packages: Bioconductor (06:01:24): > http://bioconductor.org/packages/treeio/ treeio Base Classes and Functions for Phylogenetic Tree Input and OutputBase classes and functions for parsing and exporting phylogenetic trees.link - Attachment (Bioconductor): treeio (development version) > Base classes and functions for parsing and exporting phylogenetic trees.

New Packages: Bioconductor (15:51:23): > http://bioconductor.org/packages/MAST/ MAST Model-based Analysis of Single Cell TranscriptomicsMethods and models for handling zero-inflated single cell assay data.link - Attachment (Bioconductor): MAST > Methods and models for handling zero-inflated single cell assay data.

New Packages: Bioconductor (20:51:25): > http://bioconductor.org/packages/KEGGlincs/ KEGGlincs Visualize all edges within a KEGG pathway and overlay LINCS data [option]See what is going on ‘under the hood’ of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.link - Attachment (Bioconductor): KEGGlincs > See what is going on ‘under the hood’ of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.

2017-03-01

New Packages: Bioconductor (10:51:23): > http://bioconductor.org/packages/MCbiclust/ MCbiclust Massive correlating biclusters for gene expression data and associated methodsCustom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.link - Attachment (Bioconductor): MCbiclust (development version) > Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

New Packages: Bioconductor (15:51:23): > http://bioconductor.org/packages/bigmelon/ bigmelon Illumina methylation array analysis for large experimentsMethods for working with Illumina arrays using gdsfmt.link - Attachment (Bioconductor): bigmelon > Methods for working with Illumina arrays using gdsfmt.

New Packages: Bioconductor (15:51:24): > http://bioconductor.org/packages/EventPointer/ EventPointer Identification and statistical analysis of alternative splicing events using junction arrays or RNASeq dataEventPointer is a software to identify alternative splicing events in complex experimental designs such as time course and paired samples studies. The algorithm can be applied to both data from Affymetrix arrays and Sequencing (RNASeq) data.link - Attachment (Bioconductor): EventPointer (development version) > EventPointer is a software to identify alternative splicing events in complex experimental designs such as time course and paired samples studies. The algorithm can be applied to both data from Affymetrix arrays and Sequencing (RNASeq) data.

New Packages: Bioconductor (20:51:26): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version)

2017-03-02

New Packages: Bioconductor (00:51:26): > http://bioconductor.org/packages/meshes/ meshes MeSH Enrichment and Semantic analysesMeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide…

New Packages: Bioconductor (00:51:26): > http://bioconductor.org/packages/treeio/ treeio Base Classes and Functions for Phylogenetic Tree Input and OutputBase classes and functions for parsing and exporting phylogenetic trees.link - Attachment (Bioconductor): treeio (development version) > Base classes and functions for parsing and exporting phylogenetic trees.

New Packages: Bioconductor (06:01:24): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (15:51:22): > http://bioconductor.org/packages/recount/ recount Explore and download data from the recount projectExplore and download data from the recount project available athttps://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression…

2017-03-03

New Packages: Bioconductor (10:51:24): > http://bioconductor.org/packages/coseq/ coseq Co-Expression Analysis of Sequencing DataCo-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.link - Attachment (Bioconductor): coseq (development version) > Gaussian and Poisson mixture models are implemented to cluster biological entities (e.g., genes) from high-throughput sequencing data. Parameter estimation is performed using the EM algorithm and model selection criteria (to choose the number of clusters) are provided.

New Packages: Bioconductor (16:11:25): > http://bioconductor.org/packages/recount/ recount Explore and download data from the recount projectExplore and download data from the recount project available athttps://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression…

2017-03-06

New Packages: Bioconductor (11:01:24): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version)

2017-03-07

New Packages: Bioconductor (15:51:23): > http://bioconductor.org/packages/EventPointer/ EventPointer Identification and statistical analysis of alternative splicing events using junction arrays or RNASeq dataEventPointer is a software to identify alternative splicing events in complex experimental designs such as time course and paired samples studies. The algorithm can be applied to both data from Affymetrix arrays and Sequencing (RNASeq) data.link - Attachment (Bioconductor): EventPointer (development version) > EventPointer is a software to identify alternative splicing events in complex experimental designs such as time course and paired samples studies. The algorithm can be applied to both data from Affymetrix arrays and Sequencing (RNASeq) data.

2017-03-08

New Packages: Bioconductor (00:51:44): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version)

New Packages: Bioconductor (10:56:23): > http://bioconductor.org/packages/proFIA/ proFIA Preprocessing of FIA-HRMS dataFlow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and…

New Packages: Bioconductor (15:51:24): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version)

New Packages: Bioconductor (20:46:25): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version)

2017-03-09

New Packages: Bioconductor (15:56:23): > http://bioconductor.org/packages/scDD/ scDD Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributionsThis package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.link - Attachment (Bioconductor): scDD (development version) > This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.

2017-03-10

New Packages: Bioconductor (10:51:25): > http://bioconductor.org/packages/proFIA/ proFIA Preprocessing of FIA-HRMS dataFlow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and…

2017-03-11

New Packages: Bioconductor (15:51:26): > http://bioconductor.org/packages/annotatr/ annotatr Annotation of Genomic Regions to Genomic AnnotationsGiven a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5’UTRs, exons, introns, and 3’UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic…

2017-03-13

New Packages: Bioconductor (00:51:25): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version)

New Packages: Bioconductor (10:51:23): > http://bioconductor.org/packages/EventPointer/ EventPointer Identification and statistical analysis of alternative splicing events using junction arrays or RNASeq dataEventPointer is a software to identify alternative splicing events in complex experimental designs such as time course and paired samples studies. The algorithm can be applied to both data from Affymetrix arrays and Sequencing (RNASeq) data.link - Attachment (Bioconductor): EventPointer (development version) > EventPointer is a software to identify alternative splicing events in complex experimental designs such as time course and paired samples studies. The algorithm can be applied to both data from Affymetrix arrays and Sequencing (RNASeq) data.

New Packages: Bioconductor (15:56:26): > http://bioconductor.org/packages/annotatr/ annotatr Annotation of Genomic Regions to Genomic AnnotationsGiven a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5’UTRs, exons, introns, and 3’UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic…

New Packages: Bioconductor (15:56:26): > http://bioconductor.org/packages/EventPointer/ EventPointer Identification and statistical analysis of alternative splicing events using junction arrays or RNASeq dataEventPointer is a software to identify alternative splicing events in complex experimental designs such as time course and paired samples studies. The algorithm can be applied to both data from Affymetrix arrays and Sequencing (RNASeq) data.link - Attachment (Bioconductor): EventPointer (development version) > EventPointer is a software to identify alternative splicing events in complex experimental designs such as time course and paired samples studies. The algorithm can be applied to both data from Affymetrix arrays and Sequencing (RNASeq) data.

2017-03-14

New Packages: Bioconductor (00:56:25): > http://bioconductor.org/packages/SPLINTER/ SPLINTER Splice Interpreter Of TranscriptsSPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.link - Attachment (Bioconductor): SPLINTER > SPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.

New Packages: Bioconductor (15:56:24): > http://bioconductor.org/packages/KEGGlincs/ KEGGlincs Visualize all edges within a KEGG pathway and overlay LINCS data [option]See what is going on ‘under the hood’ of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.link - Attachment (Bioconductor): KEGGlincs > See what is going on ‘under the hood’ of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.

New Packages: Bioconductor (15:56:24): > http://bioconductor.org/packages/proFIA/ proFIA Preprocessing of FIA-HRMS dataFlow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and…

2017-03-15

New Packages: Bioconductor (00:51:29): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (05:56:24): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version)

New Packages: Bioconductor (10:47:25): > http://bioconductor.org/packages/proFIA/ proFIA Preprocessing of FIA-HRMS dataFlow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and…

New Packages: Bioconductor (10:47:25): > http://bioconductor.org/packages/karyoploteR/ karyoploteR Karyotype plots with arbitrary datakaryoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.link - Attachment (Bioconductor): karyoploteR (development version) > karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

New Packages: Bioconductor (10:47:25): > http://bioconductor.org/packages/MCbiclust/ MCbiclust Massive correlating biclusters for gene expression data and associated methodsCustom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.link - Attachment (Bioconductor): MCbiclust (development version) > Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

New Packages: Bioconductor (15:56:23): > http://bioconductor.org/packages/bigmelon/ bigmelon Illumina methylation array analysis for large experimentsMethods for working with Illumina arrays using gdsfmt.link - Attachment (Bioconductor): bigmelon > Methods for working with Illumina arrays using gdsfmt.

New Packages: Bioconductor (15:56:23): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version)

2017-03-16

New Packages: Bioconductor (10:51:23): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

2017-03-17

New Packages: Bioconductor (10:46:21): > http://bioconductor.org/packages/bigmelon/ bigmelon Illumina methylation array analysis for large experimentsMethods for working with Illumina arrays using gdsfmt.link - Attachment (Bioconductor): bigmelon > Methods for working with Illumina arrays using gdsfmt.

2017-03-18

New Packages: Bioconductor (10:56:27): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (15:46:25): > http://bioconductor.org/packages/LINC/ LINC co-expression of lincRNAs and protein-coding genesThis package provides methods to compute co-expression networks of lincRNAs and protein-coding genes. Biological terms associated with the sets of protein-coding genes predict the biological contexts of lincRNAs according to the ‘Guilty by Association’ approach.link - Attachment (Bioconductor): LINC > This package provides methods to compute co-expression networks of lincRNAs and protein-coding genes. Biological terms associated with the sets of protein-coding genes predict the biological contexts of lincRNAs according to the ‘Guilty by Association’ approach.

2017-03-20

New Packages: Bioconductor (06:06:23): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (06:06:23): > http://bioconductor.org/packages/splatter/ splatter Simple Simulation of Single-cell RNA Sequencing DataSplatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented.link - Attachment (Bioconductor): splatter (development version) > Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented.

New Packages: Bioconductor (10:46:22): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

2017-03-21

New Packages: Bioconductor (06:01:21): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (06:01:21): > http://bioconductor.org/packages/proFIA/ proFIA Preprocessing of FIA-HRMS dataFlow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and…

New Packages: Bioconductor (11:01:21): > http://bioconductor.org/packages/scDD/ scDD Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributionsThis package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.link - Attachment (Bioconductor): scDD (development version) > This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.

New Packages: Bioconductor (11:01:21): > http://bioconductor.org/packages/karyoploteR/ karyoploteR Karyotype plots with arbitrary datakaryoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.link - Attachment (Bioconductor): karyoploteR (development version) > karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

New Packages: Bioconductor (15:56:21): > http://bioconductor.org/packages/flowPloidy/ flowPloidy Analyze flow cytometer data to determine sample ploidyDetermine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.link - Attachment (Bioconductor): flowPloidy > Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.

New Packages: Bioconductor (15:56:21): > http://bioconductor.org/packages/twoddpcr/ twoddpcr Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting moleculesThe twoddpcr package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad’s QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data. Previous work includes ‘definetherain’ (Jones et al., 2014) and ‘ddpcRquant’…

New Packages: Bioconductor (15:56:21): > http://bioconductor.org/packages/EventPointer/ EventPointer An effective identification of alternative splicing events using junction arrays and RNA-Seq dataEventPointer is an R package to identify alternative splicing events in complex experimental designs such as time course and paired samples studies. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software retrieves a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative 3’,…,etc), genomic position, statistical significance and percent spliced in…

2017-03-22

New Packages: Bioconductor (05:51:23): > http://bioconductor.org/packages/splatter/ splatter Simple Simulation of Single-cell RNA Sequencing DataSplatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented.link - Attachment (Bioconductor): splatter (development version) > Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented.

New Packages: Bioconductor (05:51:23): > http://bioconductor.org/packages/REMP/ REMP Repetitive Element Methylation PredictionMachine learing-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE. > > <a…

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/EventPointer/ EventPointer An effective identification of alternative splicing events using junction arrays and RNA-Seq dataEventPointer is an R package to identify alternative splicing events in complex experimental designs such as time course and paired samples studies. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software retrieves a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative 3’,…,etc), genomic position, statistical significance and percent spliced in…

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/motifcounter/ motifcounter R package for analysing TFBSs in DNA sequences‘motifcounter’ provides functionality to compute the statistics related with motif matching and counting of motif matches in DNA sequences. As an input, ‘motifcounter’ requires a motif in terms of a position frequency matrix (PFM). Furthermore, a set of DNA sequences is required to estimated a higher-order background model (BGM). The package provides functions to investigate the the per-position and per strand log-likelihood scores between the PFM and the BGM across a given sequence of set of…

2017-03-23

New Packages: Bioconductor (10:56:21): > http://bioconductor.org/packages/yamss/ yamss Tools for high-throughput metabolomicsTools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.link - Attachment (Bioconductor): yamss > Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.

New Packages: Bioconductor (10:56:21): > http://bioconductor.org/packages/proFIA/ proFIA Preprocessing of FIA-HRMS dataFlow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and…

New Packages: Bioconductor (10:56:21): > http://bioconductor.org/packages/karyoploteR/ karyoploteR Karyotype plots with arbitrary datakaryoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.link - Attachment (Bioconductor): karyoploteR (development version) > karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

New Packages: Bioconductor (15:56:21): > http://bioconductor.org/packages/KEGGlincs/ KEGGlincs Visualize all edges within a KEGG pathway and overlay LINCS data [option]See what is going on ‘under the hood’ of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.link - Attachment (Bioconductor): KEGGlincs > See what is going on ‘under the hood’ of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.

New Packages: Bioconductor (15:56:22): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

2017-03-24

New Packages: Bioconductor (05:56:20): > http://bioconductor.org/packages/ramwas/ ramwas Fast Methylome-Wide Association Study Pipeline for Enrichment PlatformsRaMWAS provides a complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association…

2017-03-25

New Packages: Bioconductor (10:51:25): > http://bioconductor.org/packages/splatter/ splatter Simple Simulation of Single-cell RNA Sequencing DataSplatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented.link - Attachment (Bioconductor): splatter (development version) > Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented.

2017-03-26

New Packages: Bioconductor (00:51:25): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

2017-03-27

New Packages: Bioconductor (01:01:24): > http://bioconductor.org/packages/meshes/ meshes MeSH Enrichment and Semantic analysesMeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide…

New Packages: Bioconductor (01:01:24): > http://bioconductor.org/packages/treeio/ treeio Base Classes and Functions for Phylogenetic Tree Input and OutputBase classes and functions for parsing and exporting phylogenetic trees.link - Attachment (Bioconductor): treeio (development version) > Base classes and functions for parsing and exporting phylogenetic trees.

New Packages: Bioconductor (05:51:23): > http://bioconductor.org/packages/SPLINTER/ SPLINTER Splice Interpreter Of TranscriptsSPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.link - Attachment (Bioconductor): SPLINTER > SPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.

New Packages: Bioconductor (05:51:23): > http://bioconductor.org/packages/treeio/ treeio Base Classes and Functions for Phylogenetic Tree Input and OutputBase classes and functions for parsing and exporting phylogenetic trees.link - Attachment (Bioconductor): treeio (development version) > Base classes and functions for parsing and exporting phylogenetic trees.

New Packages: Bioconductor (10:51:22): > http://bioconductor.org/packages/twoddpcr/ twoddpcr Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting moleculesThe twoddpcr package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad’s QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data. Previous work includes ‘definetherain’ (Jones et al., 2014) and ‘ddpcRquant’…

New Packages: Bioconductor (15:51:22): > http://bioconductor.org/packages/EventPointer/ EventPointer An effective identification of alternative splicing events using junction arrays and RNA-Seq dataEventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software retrieves a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative…

2017-03-28

New Packages: Bioconductor (05:56:22): > http://bioconductor.org/packages/splatter/ splatter Simple Simulation of Single-cell RNA Sequencing DataSplatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented.link - Attachment (Bioconductor): splatter (development version) > Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented.

New Packages: Bioconductor (10:51:23): > http://bioconductor.org/packages/coseq/ coseq Co-Expression Analysis of Sequencing DataCo-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.link - Attachment (Bioconductor): coseq (development version) > Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.

New Packages: Bioconductor (10:51:24): > http://bioconductor.org/packages/DaMiRseq/ DaMiRseq Data Mining for RNA-seq data: normalization, feature selection and classificationThe DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them for classification purposes.. The package accepts any kind of data presented as a table of raw counts and allows including covariates that occur with the experimental setting. A series of functions enable the user to clean up the data by filtering genomic features and samples, to adjust data by identifying and removing the unwanted source of variation (i.e….

New Packages: Bioconductor (21:01:23): > http://bioconductor.org/packages/Pi/ Pi Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network LevelPriority index or Pi is developed as a genomic-led target prioritisation system, with the focus on leveraging human genetic data to prioritise potential drug targets at the gene, pathway and network level. The long term goal is to use such information to enhance early-stage target validation. Based on evidence of disease association from genome-wide association studies (GWAS), this prioritisation system is able to generate evidence to support identification of the specific modulated genes…

2017-03-29

New Packages: Bioconductor (06:01:29): > http://bioconductor.org/packages/proFIA/ proFIA Preprocessing of FIA-HRMS dataFlow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and…

New Packages: Bioconductor (10:56:22): > http://bioconductor.org/packages/BiocWorkflowTools/ BiocWorkflowTools Tools to aid the development of Bioconductor Workflow packagesProvides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.link - Attachment (Bioconductor): BiocWorkflowTools > Provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.

New Packages: Bioconductor (15:51:22): > http://bioconductor.org/packages/flowPloidy/ flowPloidy Analyze flow cytometer data to determine sample ploidyDetermine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.link - Attachment (Bioconductor): flowPloidy > Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.

2017-03-30

New Packages: Bioconductor (05:51:22): > http://bioconductor.org/packages/EventPointer/ EventPointer An effective identification of alternative splicing events using junction arrays and RNA-Seq dataEventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative…

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/karyoploteR/ karyoploteR Karyotype plots with arbitrary datakaryoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.link - Attachment (Bioconductor): karyoploteR (development version) > karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

New Packages: Bioconductor (15:51:21): > http://bioconductor.org/packages/IntEREst/ IntEREst Intron-Exon Retention EstimatorThis package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).link - Attachment (Bioconductor): IntEREst (development version) > This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).

New Packages: Bioconductor (21:01:23): > http://bioconductor.org/packages/KEGGlincs/ KEGGlincs Visualize all edges within a KEGG pathway and overlay LINCS data [option]See what is going on ‘under the hood’ of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.link - Attachment (Bioconductor): KEGGlincs > See what is going on ‘under the hood’ of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.

2017-03-31

New Packages: Bioconductor (06:01:28): > http://bioconductor.org/packages/SPLINTER/ SPLINTER Splice Interpreter Of TranscriptsSPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.link - Attachment (Bioconductor): SPLINTER > SPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.

New Packages: Bioconductor (06:01:28): > http://bioconductor.org/packages/karyoploteR/ karyoploteR Plot customizable linear genomes displaying arbitrary datakaryoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.link - Attachment (Bioconductor): karyoploteR (development version) > karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

New Packages: Bioconductor (10:51:23): > http://bioconductor.org/packages/BiocWorkflowTools/ BiocWorkflowTools Tools to aid the development of Bioconductor Workflow packagesProvides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.link - Attachment (Bioconductor): BiocWorkflowTools > Provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.

New Packages: Bioconductor (10:51:23): > http://bioconductor.org/packages/statTarget/ statTarget Statistical Analysis of Metabolite ProfileAn easy to use tool provides a graphical user interface for quality control based shift signal correction, integration of metabolomic data from multi-batch experiments, and the comprehensive statistic analysis in non-targeted or targeted metabolomics.link - Attachment (Bioconductor): statTarget > An easy to use tool provides a graphical user interface for quality control based shift signal correction, integration of metabolomic data from multi-batch experiments, and the comprehensive statistic analysis in non-targeted or targeted metabolomics.

New Packages: Bioconductor (10:51:23): > http://bioconductor.org/packages/IntEREst/ IntEREst Intron-Exon Retention EstimatorThis package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).link - Attachment (Bioconductor): IntEREst (development version) > This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).

New Packages: Bioconductor (20:56:24): > http://bioconductor.org/packages/samExploreR/ samExploreR samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulationThis R package is designed for subsampling procedure to simulate sequencing experiments with reduced sequencing depth. This package can be used to anlayze data generated from all major sequencing platforms such as Illumina GA, HiSeq, MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM Proton sequencers. It supports multiple operating systems incluidng Linux, Mac OS X, FreeBSD and Solaris. Was developed with usage of Rsubread.link - Attachment (Bioconductor): samExploreR (development version) > This R package is designed for subsampling procedure to simulate sequencing experiments with reduced sequencing depth. This package can be used to anlayze data generated from all major sequencing platforms such as Illumina GA, HiSeq, MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM Proton sequencers. It supports multiple operating systems incluidng Linux, Mac OS X, FreeBSD and Solaris. Was developed with usage of Rsubread.

2017-04-02

New Packages: Bioconductor (19:36:31): > http://bioconductor.org/packages/cellscape/ cellscape Explores single cell copy number profiles in the context of a single cell treeCellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of…

New Packages: Bioconductor (20:51:24): > http://bioconductor.org/packages/regsplice/ regsplice L1-regularization based methods for detection of differential splicingStatistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.link - Attachment (Bioconductor): regsplice > Statistical methods for detection of differential exon usage in RNA-seq and exon microarray data sets, using L1 regularization (lasso) to improve power.

2017-04-03

New Packages: Bioconductor (06:01:23): > http://bioconductor.org/packages/regsplice/ regsplice L1-regularization based methods for detection of differential splicingStatistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.link - Attachment (Bioconductor): regsplice > Statistical methods for detection of differential exon usage in RNA-seq and exon microarray data sets, using L1 regularization (lasso) to improve power.

New Packages: Bioconductor (06:01:23): > http://bioconductor.org/packages/treeio/ treeio Base Classes and Functions for Phylogenetic Tree Input and OutputBase classes and functions for parsing and exporting phylogenetic trees.link - Attachment (Bioconductor): treeio (development version) > Base classes and functions for parsing and exporting phylogenetic trees.

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/treeio/ treeio Base Classes and Functions for Phylogenetic Tree Input and OutputBase classes and functions for parsing and exporting phylogenetic trees.link - Attachment (Bioconductor): treeio (development version) > Base classes and functions for parsing and exporting phylogenetic trees.

New Packages: Bioconductor (15:51:20): > http://bioconductor.org/packages/BUMHMM/ BUMHMM Computational pipeline for computing probability of modification from structure probing experiment dataThis is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a “drop-off rate” for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of…

New Packages: Bioconductor (15:51:20): > http://bioconductor.org/packages/cydar/ cydar Using Mass Cytometry for Differential Abundance AnalysesIdentifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.link - Attachment (Bioconductor): cydar (development version) > Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.

New Packages: Bioconductor (20:56:23): > http://bioconductor.org/packages/gcapc/ gcapc GC Aware Peak CallerPeak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated using generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.link - Attachment (Bioconductor): gcapc (development version) > Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated using generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.

2017-04-04

New Packages: Bioconductor (10:51:23): > http://bioconductor.org/packages/BUMHMM/ BUMHMM Computational pipeline for computing probability of modification from structure probing experiment dataThis is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a “drop-off rate” for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of…

New Packages: Bioconductor (15:56:22): > http://bioconductor.org/packages/GOpro/ GOpro Find the most characteristic gene ontology terms for groups of human genesFind the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 Group (http://mi2.mini.pw.edu.pl/,https://github.com/geneticsMiNIng).link - Attachment (GitHub): geneticsMiNIng: Research group from Warsaw University of Technology > GitHub is where people build software. More than 21 million people use GitHub to discover, fork, and contribute to over 56 million projects. - Attachment (Bioconductor): GOpro > Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 Group (http://mi2.mini.pw.edu.pl/, https://github.com/geneticsMiNIng).

New Packages: Bioconductor (15:56:22): > http://bioconductor.org/packages/MAST/ MAST Model-based Analysis of Single Cell TranscriptomicsMethods and models for handling zero-inflated single cell assay data.link - Attachment (Bioconductor): MAST > Methods and models for handling zero-inflated single cell assay data.

New Packages: Bioconductor (15:56:22): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache (development version) > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

2017-04-05

New Packages: Bioconductor (05:56:23): > http://bioconductor.org/packages/BUMHMM/ BUMHMM Computational pipeline for computing probability of modification from structure probing experiment dataThis is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a “drop-off rate” for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of…

New Packages: Bioconductor (20:56:23): > http://bioconductor.org/packages/RJMCMCNucleosomes/ RJMCMCNucleosomes Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.link - Attachment (Bioconductor): RJMCMCNucleosomes (development version) > This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.

2017-04-06

New Packages: Bioconductor (10:51:23): > http://bioconductor.org/packages/GOpro/ GOpro Find the most characteristic gene ontology terms for groups of human genesFind the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 Group (http://mi2.mini.pw.edu.pl/,https://github.com/geneticsMiNIng).link - Attachment (GitHub): geneticsMiNIng: Research group from Warsaw University of Technology > GitHub is where people build software. More than 21 million people use GitHub to discover, fork, and contribute to over 56 million projects. - Attachment (Bioconductor): GOpro > Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 Group (http://mi2.mini.pw.edu.pl/, https://github.com/geneticsMiNIng).

New Packages: Bioconductor (15:51:20): > http://bioconductor.org/packages/MutationalPatterns/ MutationalPatterns Studying patterns in base substitution cataloguesAn extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.link - Attachment (Bioconductor): MutationalPatterns > An extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.

New Packages: Bioconductor (15:51:21): > http://bioconductor.org/packages/coseq/ coseq Co-Expression Analysis of Sequencing DataCo-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.link - Attachment (Bioconductor): coseq (development version) > Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.

New Packages: Bioconductor (21:06:22): > http://bioconductor.org/packages/SIMLR/ SIMLR Title: SIMLR: Single-cell Interpretation via Multi-kernel LeaRningSingle-cell RNA-seq technologies enable high throughput gene expression measurement of individual cells, and allow the discovery of heterogeneity within cell populations. Measurement of cell-to-cell gene expression similarity is critical to identification, visualization and analysis of cell populations. However, single-cell data introduce challenges to conventional measures of gene expression similarity because of the high level of noise, outliers and dropouts. We develop a novel…

New Packages: Bioconductor (21:06:23): > http://bioconductor.org/packages/DEsubs/ DEsubs DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experimentsDEsubs is a network-based systems biology package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customizable framework covering a broad range of operation modes at all stages of the subpathway analysis, enabling a case-specific approach. The operation modes refer to the pathway network construction and processing, the subpathway extraction, visualization and enrichment analysis with regard to various…

New Packages: Bioconductor (21:06:23): > http://bioconductor.org/packages/matter/ matter A framework for rapid prototyping with binary data on diskMemory-efficient reading, writing, and manipulation of structured binary data on disk as vectors, matrices, and arrays.link - Attachment (Bioconductor): matter > Memory-efficient reading, writing, and manipulation of structured binary data on disk as vectors, matrices, and arrays. This package is designed to be used as a back-end for Cardinal for working with high-resolution mass spectrometry imaging data.

New Packages: Bioconductor (21:06:23): > http://bioconductor.org/packages/coseq/ coseq Co-Expression Analysis of Sequencing DataCo-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.link - Attachment (Bioconductor): coseq (development version) > Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.

2017-04-07

New Packages: Bioconductor (01:01:23): > http://bioconductor.org/packages/ramwas/ ramwas Fast Methylome-Wide Association Study Pipeline for Enrichment PlatformsRaMWAS provides a complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association…

New Packages: Bioconductor (06:01:23): > http://bioconductor.org/packages/wiggleplotr/ wiggleplotr Make read coverage plots from BigWig filesTools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.link - Attachment (Bioconductor): wiggleplotr (development version) > Tools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (16:01:21): > http://bioconductor.org/packages/flowPloidy/ flowPloidy Analyze flow cytometer data to determine sample ploidyDetermine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.link - Attachment (Bioconductor): flowPloidy > Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.

New Packages: Bioconductor (16:01:21): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (16:01:21): > http://bioconductor.org/packages/RJMCMCNucleosomes/ RJMCMCNucleosomes Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.link - Attachment (Bioconductor): RJMCMCNucleosomes (development version) > This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.

2017-04-08

New Packages: Bioconductor (00:56:25): > http://bioconductor.org/packages/gcapc/ gcapc GC Aware Peak CallerPeak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.link - Attachment (Bioconductor): gcapc (development version) > Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated using generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.

New Packages: Bioconductor (06:06:26): > http://bioconductor.org/packages/GOpro/ GOpro Find the most characteristic gene ontology terms for groups of human genesFind the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 Group (http://mi2.mini.pw.edu.pl/,https://github.com/geneticsMiNIng).link - Attachment (GitHub): geneticsMiNIng: Research group from Warsaw University of Technology > GitHub is where people build software. More than 21 million people use GitHub to discover, fork, and contribute to over 56 million projects. - Attachment (Bioconductor): GOpro > Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 Group (http://mi2.mini.pw.edu.pl/, https://github.com/geneticsMiNIng).

New Packages: Bioconductor (16:06:25): > http://bioconductor.org/packages/TVTB/ TVTB TVTB: The VCF Tool BoxThe package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).link - Attachment (Bioconductor): TVTB > The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).

New Packages: Bioconductor (16:06:25): > http://bioconductor.org/packages/chimeraviz/ chimeraviz Visualization tools for gene fusionschimeraviz manages data from fusion gene finders and provides useful visualization tools.link - Attachment (Bioconductor): chimeraviz (development version) > chimeraviz manages data from fusion gene finders and provides useful visualization tools.

2017-04-09

New Packages: Bioconductor (01:01:25): > http://bioconductor.org/packages/scone/ scone Single Cell Overview of Normalized Expression dataSCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.link - Attachment (Bioconductor): scone (development version) > SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.

New Packages: Bioconductor (11:01:24): > http://bioconductor.org/packages/cydar/ cydar Using Mass Cytometry for Differential Abundance AnalysesIdentifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.link - Attachment (Bioconductor): cydar (development version) > Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.

2017-04-10

New Packages: Bioconductor (00:51:23): > http://bioconductor.org/packages/gcapc/ gcapc GC Aware Peak CallerPeak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.link - Attachment (Bioconductor): gcapc (development version) > Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.

New Packages: Bioconductor (11:01:21): > http://bioconductor.org/packages/flowPloidy/ flowPloidy Analyze flow cytometer data to determine sample ploidyDetermine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.link - Attachment (Bioconductor): flowPloidy > Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.

New Packages: Bioconductor (11:01:21): > http://bioconductor.org/packages/BUMHMM/ BUMHMM Computational pipeline for computing probability of modification from structure probing experiment dataThis is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a “drop-off rate” for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of…

New Packages: Bioconductor (11:01:21): > http://bioconductor.org/packages/NADfinder/ NADfinder Call wide peaks for sequencing dataCall peaks for two samples: target and control. It will count the reads for tiles of the genome and then convert it to ratios. The ratios will be corrected and smoothed. The z-scores is calculated for each counting windows over the background. The peaks will be detected based on z-scores.link - Attachment (Bioconductor): NADfinder (development version) > Call peaks for two samples: target and control. It will count the reads for tiles of the genome and then convert it to ratios. The ratios will be corrected and smoothed. The z-scores is calculated for each counting windows over the background. The peaks will be detected based on z-scores.

New Packages: Bioconductor (15:56:21): > http://bioconductor.org/packages/scDD/ scDD Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributionsThis package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.link - Attachment (Bioconductor): scDD (development version) > This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.

New Packages: Bioconductor (15:56:21): > http://bioconductor.org/packages/GA4GHclient/ GA4GHclient A Bioconductor package for accessing GA4GH API data serversGA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.link - Attachment (Bioconductor): GA4GHclient (development version) > GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.

New Packages: Bioconductor (21:06:23): > http://bioconductor.org/packages/flowPloidy/ flowPloidy Analyze flow cytometer data to determine sample ploidyDetermine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.link - Attachment (Bioconductor): flowPloidy > Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.

New Packages: Bioconductor (21:06:23): > http://bioconductor.org/packages/TVTB/ TVTB TVTB: The VCF Tool BoxThe package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).link - Attachment (Bioconductor): TVTB > The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).

2017-04-11

New Packages: Bioconductor (00:51:22): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (00:51:23): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (05:51:23): > http://bioconductor.org/packages/ramwas/ ramwas Fast Methylome-Wide Association Study Pipeline for Enrichment PlatformsRaMWAS provides a complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association…

New Packages: Bioconductor (05:51:23): > http://bioconductor.org/packages/EventPointer/ EventPointer An effective identification of alternative splicing events using junction arrays and RNA-Seq dataEventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative…

New Packages: Bioconductor (11:01:22): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

2017-04-12

New Packages: Bioconductor (00:56:23): > http://bioconductor.org/packages/ramwas/ ramwas Fast Methylome-Wide Association Study Pipeline for Enrichment PlatformsRaMWAS provides a complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association…

New Packages: Bioconductor (06:06:21): > http://bioconductor.org/packages/karyoploteR/ karyoploteR Plot customizable linear genomes displaying arbitrary datakaryoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.link - Attachment (Bioconductor): karyoploteR (development version) > karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

New Packages: Bioconductor (10:56:22): > http://bioconductor.org/packages/MutationalPatterns/ MutationalPatterns Studying patterns in base substitution cataloguesAn extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.link - Attachment (Bioconductor): MutationalPatterns > An extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.

New Packages: Bioconductor (10:56:22): > http://bioconductor.org/packages/EventPointer/ EventPointer An effective identification of alternative splicing events using junction arrays and RNA-Seq dataEventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative…

New Packages: Bioconductor (10:56:22): > http://bioconductor.org/packages/semisup/ semisup Detecting SNPs with interactive effects on a quantitative traitThis R packages moves away from testing interaction terms, and move towards testing whether an individual SNP is involved in any interaction. This reduces the multiple testing burden to one test per SNP, and allows for interactions with unobserved factors. Analysing one SNP at a time, it splits the individuals into two groups, based on the number of minor alleles. If the quantitative trait differs in mean between the two groups, the SNP has a main effect. If the quantitative trait differs in…

2017-04-13

New Packages: Bioconductor (00:51:23): > http://bioconductor.org/packages/psichomics/ psichomics Graphical Interface for Alternative Splicing Quantification, Analysis and VisualisationInteractive R package with a Shiny-based graphical interface for the quantification, analysis and visualisation of alternative splicing data from The Cancer Genome Atlas (TCGA) or the Genotype-Tissue Expression (GTEx) project. This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA and GTEx samples. > > <a…

New Packages: Bioconductor (00:51:24): > http://bioconductor.org/packages/annotatr/ annotatr Annotation of Genomic Regions to Genomic AnnotationsGiven a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5’UTRs, exons, introns, and 3’UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic…

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/IMAS/ IMAS Integrative analysis of Multi-omics data for Alternative SplicingIntegrative analysis of Multi-omics data for Alternative splicing.link - Attachment (Bioconductor): IMAS (development version) > Integrative analysis of Multi-omics data for Alternative splicing.

New Packages: Bioconductor (15:51:22): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (20:56:22): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

2017-04-14

New Packages: Bioconductor (05:51:23): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (11:06:22): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (15:51:21): > http://bioconductor.org/packages/scDD/ scDD Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributionsThis package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.link - Attachment (Bioconductor): scDD (development version) > This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.

New Packages: Bioconductor (15:51:22): > http://bioconductor.org/packages/IMAS/ IMAS Integrative analysis of Multi-omics data for Alternative SplicingIntegrative analysis of Multi-omics data for Alternative splicing.link - Attachment (Bioconductor): IMAS (development version) > Integrative analysis of Multi-omics data for Alternative splicing.

New Packages: Bioconductor (20:56:24): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

2017-04-15

New Packages: Bioconductor (16:01:24): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/annotatr/ annotatr Annotation of Genomic Regions to Genomic AnnotationsGiven a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5’UTRs, exons, introns, and 3’UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic…

2017-04-16

2017-04-17

New Packages: Bioconductor (15:51:21): > http://bioconductor.org/packages/MoonlightR/ MoonlightR Identify oncogenes and tumor suppressor genes from omics dataMotivation: The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). Results: We present an R/bioconductor package called MoonlightR which returns a list of candidate driver genes for specific cancer types on the basis of TCGA expression data. The method first infers gene regulatory networks and then carries out a functional enrichment analysis…

New Packages: Bioconductor (15:51:21): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.link - Attachment (Bioconductor): MWASTools (development version) > MWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.

New Packages: Bioconductor (15:51:21): > http://bioconductor.org/packages/ChIPexoQual/ ChIPexoQual ChIPexoQualPackage with a quality control pipeline for ChIP-exo/nexus data.link - Attachment (Bioconductor): ChIPexoQual (development version) > Package with a quality control pipeline for ChIP-exo/nexus data.

New Packages: Bioconductor (15:51:21): > http://bioconductor.org/packages/rqt/ rqt rqt: utilities for gene-level meta-analysisDespite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: “Gene-set association tests for next-generation sequencing data” by Lee et al (2016), Bioinformatics, 32(17), i611-i619,http://bioconductor.org/packages/rqt/ - Attachment (Bioconductor): rqt (development version) > Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see:

New Packages: Bioconductor (15:51:21): > http://bioconductor.org/packages/GA4GHclient/ GA4GHclient A Bioconductor package for accessing GA4GH API data serversGA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.link - Attachment (Bioconductor): GA4GHclient (development version) > GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.

New Packages: Bioconductor (15:51:21): > http://bioconductor.org/packages/wiggleplotr/ wiggleplotr Make read coverage plots from BigWig filesTools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.link - Attachment (Bioconductor): wiggleplotr (development version) > Tools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.

2017-04-18

New Packages: Bioconductor (01:01:23): > http://bioconductor.org/packages/cellscape/ cellscape Explores single cell copy number profiles in the context of a single cell treeCellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of…

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/MutationalPatterns/ MutationalPatterns Studying patterns in base substitution cataloguesAn extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.link - Attachment (Bioconductor): MutationalPatterns > An extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.

New Packages: Bioconductor (10:51:22): > http://bioconductor.org/packages/pathprint/ pathprint Pathway fingerprinting for analysis of gene expression arraysAlgorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.link - Attachment (Bioconductor): pathprint (development version) > Algorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.

New Packages: Bioconductor (10:51:22): > http://bioconductor.org/packages/semisup/ semisup Detecting SNPs with interactive effects on a quantitative traitThis R packages moves away from testing interaction terms, and move towards testing whether an individual SNP is involved in any interaction. This reduces the multiple testing burden to one test per SNP, and allows for interactions with unobserved factors. Analysing one SNP at a time, it splits the individuals into two groups, based on the number of minor alleles. If the quantitative trait differs in mean between the two groups, the SNP has a main effect. If the quantitative trait differs in…

New Packages: Bioconductor (21:01:23): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

2017-04-19

New Packages: Bioconductor (00:56:23): > http://bioconductor.org/packages/cellscape/ cellscape Explores single cell copy number profiles in the context of a single cell treeCellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of…

New Packages: Bioconductor (00:56:23): > http://bioconductor.org/packages/timescape/ timescape Patient Clonal TimescapesTimeScape is an automated tool for navigating temporal clonal evolution data. The key attributes of this implementation involve the enumeration of clones, their evolutionary relationships and their shifting dynamics over time. TimeScape requires two inputs: (i) the clonal phylogeny and (ii) the clonal prevalences. Optionally, TimeScape accepts a data table of targeted mutations observed in each clone and their allele prevalences over time. The output is the TimeScape plot showing clonal…

New Packages: Bioconductor (11:01:21): > http://bioconductor.org/packages/metavizr/ metavizr R Interface to the metaviz web app for interactive metagenomics data analysis and visualizationThis package provides Websocket communication to the metaviz web app (http://metaviz.cbcb.umd.edu) for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported (e.g., MRexperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as… - Attachment (metaviz.cbcb.umd.edu): Metaviz > Epiviz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

New Packages: Bioconductor (15:56:21): > http://bioconductor.org/packages/IWTomics/ IWTomics Interval-Wise Testing for Omics DataImplementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in “Omics” data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.link - Attachment (Bioconductor): IWTomics (development version) > Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in

New Packages: Bioconductor (15:56:22): > http://bioconductor.org/packages/ramwas/ ramwas Fast Methylome-Wide Association Study Pipeline for Enrichment PlatformsRaMWAS provides a complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association…

2017-04-20

New Packages: Bioconductor (01:06:24): > http://bioconductor.org/packages/RTNduals/ RTNduals Analysis of co-regulatory network motifs and inference of ‘dual regulons’RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer ‘dual regulons’, a new concept that tests whether regulon pairs agree on the predicted downstream effects.link - Attachment (Bioconductor): RTNduals (development version) > RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer ‘dual regulons’, a new concept that tests whether regulon pairs agree on the predicted downstream effects.

New Packages: Bioconductor (01:06:24): > http://bioconductor.org/packages/metavizr/ metavizr R Interface to the metaviz web app for interactive metagenomics data analysis and visualizationThis package provides Websocket communication to the metaviz web app (http://metaviz.cbcb.umd.edu) for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported (e.g., MRexperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as… - Attachment (metaviz.cbcb.umd.edu): Metaviz > Epiviz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

New Packages: Bioconductor (05:51:23): > http://bioconductor.org/packages/MutationalPatterns/ MutationalPatterns Studying patterns in base substitution cataloguesAn extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.link - Attachment (Bioconductor): MutationalPatterns > An extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.

New Packages: Bioconductor (05:51:23): > http://bioconductor.org/packages/metavizr/ metavizr R Interface to the metaviz web app for interactive metagenomics data analysis and visualizationThis package provides Websocket communication to the metaviz web app (http://metaviz.cbcb.umd.edu) for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported (e.g., MRexperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as… - Attachment (metaviz.cbcb.umd.edu): Metaviz > Epiviz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

New Packages: Bioconductor (11:01:21): > http://bioconductor.org/packages/pathprint/ pathprint Pathway fingerprinting for analysis of gene expression arraysAlgorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.link - Attachment (Bioconductor): pathprint (development version) > Algorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.

New Packages: Bioconductor (15:51:24): > http://bioconductor.org/packages/MutationalPatterns/ MutationalPatterns Studying patterns in base substitution cataloguesAn extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.link - Attachment (Bioconductor): MutationalPatterns > An extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.

New Packages: Bioconductor (15:51:24): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache (development version) > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

New Packages: Bioconductor (15:51:24): > http://bioconductor.org/packages/semisup/ semisup Detecting SNPs with interactive effects on a quantitative traitThis R packages moves away from testing interaction terms, and move towards testing whether an individual SNP is involved in any interaction. This reduces the multiple testing burden to one test per SNP, and allows for interactions with unobserved factors. Analysing one SNP at a time, it splits the individuals into two groups, based on the number of minor alleles. If the quantitative trait differs in mean between the two groups, the SNP has a main effect. If the quantitative trait differs in…

New Packages: Bioconductor (21:01:22): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (21:01:22): > http://bioconductor.org/packages/methylInheritance/ methylInheritance Permutation-Based Analysis associating Conserved Differentially Methylated Elements from One Generation to the Next to a Treatment EffectPermutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.link - Attachment (Bioconductor): methylInheritance (development version) > Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.

New Packages: Bioconductor (21:01:22): > http://bioconductor.org/packages/metavizr/ metavizr R Interface to the metaviz web app for interactive metagenomics data analysis and visualizationThis package provides Websocket communication to the metaviz web app (http://metaviz.cbcb.umd.edu) for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported (e.g., MRexperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as… - Attachment (metaviz.cbcb.umd.edu): Metaviz > Epiviz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

2017-04-21

New Packages: Bioconductor (05:51:23): > http://bioconductor.org/packages/chimeraviz/ chimeraviz Visualization tools for gene fusionschimeraviz manages data from fusion gene finders and provides useful visualization tools.link - Attachment (Bioconductor): chimeraviz (development version) > chimeraviz manages data from fusion gene finders and provides useful visualization tools.

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/chimeraviz/ chimeraviz Visualization tools for gene fusionschimeraviz manages data from fusion gene finders and provides useful visualization tools.link - Attachment (Bioconductor): chimeraviz (development version) > chimeraviz manages data from fusion gene finders and provides useful visualization tools.

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/MIGSA/ MIGSA Massive and Integrative Gene Set AnalysisMassive and Integrative Gene Set Analysis. The MIGSA package allows to perform a massive and integrative gene set analysis over several expression and gene sets simultaneously. It provides a common gene expression analytic framework that grants a comprehensive and coherent analysis. Only a minimal user parameter setting is required to perform both singular and gene set enrichment analyses in an integrative manner by means of the best available methods, i.e. dEnricher and…

New Packages: Bioconductor (10:51:21): > http://bioconductor.org/packages/pathprint/ pathprint Pathway fingerprinting for analysis of gene expression arraysAlgorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.link - Attachment (Bioconductor): pathprint (development version) > Algorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.

New Packages: Bioconductor (15:56:21): > http://bioconductor.org/packages/MIGSA/ MIGSA Massive and Integrative Gene Set AnalysisMassive and Integrative Gene Set Analysis. The MIGSA package allows to perform a massive and integrative gene set analysis over several expression and gene sets simultaneously. It provides a common gene expression analytic framework that grants a comprehensive and coherent analysis. Only a minimal user parameter setting is required to perform both singular and gene set enrichment analyses in an integrative manner by means of the best available methods, i.e. dEnricher and…

New Packages: Bioconductor (21:01:23): > http://bioconductor.org/packages/chimeraviz/ chimeraviz Visualization tools for gene fusionschimeraviz manages data from fusion gene finders and provides useful visualization tools.link - Attachment (Bioconductor): chimeraviz (development version) > chimeraviz manages data from fusion gene finders and provides useful visualization tools.

New Packages: Bioconductor (21:01:23): > http://bioconductor.org/packages/timescape/ timescape Patient Clonal TimescapesTimeScape is an automated tool for navigating temporal clonal evolution data. The key attributes of this implementation involve the enumeration of clones, their evolutionary relationships and their shifting dynamics over time. TimeScape requires two inputs: (i) the clonal phylogeny and (ii) the clonal prevalences. Optionally, TimeScape accepts a data table of targeted mutations observed in each clone and their allele prevalences over time. The output is the TimeScape plot showing clonal…

2017-04-22

New Packages: Bioconductor (11:01:23): > http://bioconductor.org/packages/psichomics/ psichomics Graphical Interface for Alternative Splicing Quantification, Analysis and VisualisationInteractive R package with a Shiny-based graphical interface for the quantification, analysis and visualisation of alternative splicing data from The Cancer Genome Atlas (TCGA) or the Genotype-Tissue Expression (GTEx) project. This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA and GTEx samples. > > <a…

2017-04-23

New Packages: Bioconductor (06:06:25): > http://bioconductor.org/packages/splatter/ splatter Simple Simulation of Single-cell RNA Sequencing DataSplatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.link - Attachment (Bioconductor): splatter (development version) > Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented.

New Packages: Bioconductor (10:51:24): > http://bioconductor.org/packages/chimeraviz/ chimeraviz Visualization tools for gene fusionschimeraviz manages data from fusion gene finders and provides useful visualization tools.link - Attachment (Bioconductor): chimeraviz (development version) > chimeraviz manages data from fusion gene finders and provides useful visualization tools.

New Packages: Bioconductor (16:01:24): > http://bioconductor.org/packages/mapscape/ mapscape mapscapeMapScape integrates clonal prevalence, clonal hierarchy, anatomic and mutational information to provide interactive visualization of spatial clonal evolution. There are four inputs to MapScape: (i) the clonal phylogeny, (ii) clonal prevalences, (iii) an image reference, which may be a medical image or drawing and (iv) pixel locations for each sample on the referenced image. Optionally, MapScape can accept a data table of mutations for each clone and their variant allele frequencies in each…

New Packages: Bioconductor (20:56:24): > http://bioconductor.org/packages/coseq/ coseq Co-Expression Analysis of Sequencing DataCo-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.link - Attachment (Bioconductor): coseq (development version) > Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.

New Packages: Bioconductor (20:56:25): > http://bioconductor.org/packages/cellscape/ cellscape Explores single cell copy number profiles in the context of a single cell treeCellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of…

New Packages: Bioconductor (20:56:25): > http://bioconductor.org/packages/netReg/ netReg Network-Regularized Regression ModelsnetReg fits linear regression models using network-penalization. Graph prior knowledge, in the form of biological networks, is being incorporated into the likelihood of the linear model. The networks describe biological relationships such as co-regulation or dependency of the same transcription factors/metabolites/etc. yielding a part sparse and part smooth solution for coefficient profiles.link - Attachment (Bioconductor): netReg (development version) > netReg fits linear regression models using network-penalization. Graph prior knowledge, in the form of biological networks, is being incorporated into the likelihood of the linear model. The networks describe biological relationships such as co-regulation or dependency of the same transcription factors/metabolites/etc. yielding a part sparse and part smooth solution for coefficient profiles.

New Packages: Bioconductor (20:56:25): > http://bioconductor.org/packages/metavizr/ metavizr R Interface to the metaviz web app for interactive metagenomics data analysis and visualizationThis package provides Websocket communication to the metaviz web app (http://metaviz.cbcb.umd.edu) for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported (e.g., MRexperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as… - Attachment (metaviz.cbcb.umd.edu): Metaviz > Epiviz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

2017-04-24

New Packages: Bioconductor (05:51:22): > http://bioconductor.org/packages/pathprint/ pathprint Pathway fingerprinting for analysis of gene expression arraysAlgorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.link - Attachment (Bioconductor): pathprint (development version) > Algorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.

New Packages: Bioconductor (11:01:22): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache (development version) > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/MoonlightR/ MoonlightR Identify oncogenes and tumor suppressor genes from omics dataMotivation: The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). Results: We present an R/bioconductor package called MoonlightR which returns a list of candidate driver genes for specific cancer types on the basis of TCGA expression data. The method first infers gene regulatory networks and then carries out a functional enrichment analysis…

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/psichomics/ psichomics Graphical Interface for Alternative Splicing Quantification, Analysis and VisualisationInteractive R package with a Shiny-based graphical interface for the quantification, analysis and visualisation of alternative splicing data from The Cancer Genome Atlas (TCGA) or the Genotype-Tissue Expression (GTEx) project. This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA and GTEx samples. > > <a…

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/MutationalPatterns/ MutationalPatterns Studying patterns in base substitution cataloguesAn extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.link - Attachment (Bioconductor): MutationalPatterns > An extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/HelloRanges/ HelloRanges Introduce *Ranges to bedtools usersTranslates bedtools command-line invocations to R code calling functions from the Bioconductor Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.link - Attachment (Bioconductor): HelloRanges > Translates bedtools command-line invocations to R code calling functions from the Bioconductor Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/crisprseekplus/ crisprseekplus crisprseekplusBioinformatics platform containing interface to work with offTargetAnalysis and compare2Sequences in the CRISPRseek package, and GUIDEseqAnalysis.link - Attachment (Bioconductor): crisprseekplus > Bioinformatics platform containing interface to work with offTargetAnalysis and compare2Sequences in the CRISPRseek package, and GUIDEseqAnalysis.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/annotatr/ annotatr Annotation of Genomic Regions to Genomic AnnotationsGiven a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5’UTRs, exons, introns, and 3’UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic…

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/meshes/ meshes MeSH Enrichment and Semantic analysesMeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide…

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/M3Drop/ M3Drop Michaelis-Menten Modelling of Dropouts in single-cell RNASeqThis package fits a Michaelis-Menten model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells.link - Attachment (Bioconductor): M3Drop > This package fits a Michaelis-Menten model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/TVTB/ TVTB TVTB: The VCF Tool BoxThe package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).link - Attachment (Bioconductor): TVTB > The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/StarBioTrek/ StarBioTrek StarBioTrekThis tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.link - Attachment (Bioconductor): StarBioTrek > This tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/regsplice/ regsplice L1-regularization based methods for detection of differential splicingStatistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.link - Attachment (Bioconductor): regsplice > Statistical methods for detection of differential exon usage in RNA-seq and exon microarray data sets, using L1 regularization (lasso) to improve power.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/yamss/ yamss Tools for high-throughput metabolomicsTools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.link - Attachment (Bioconductor): yamss > Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/proFIA/ proFIA Preprocessing of FIA-HRMS dataFlow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and…

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/CCPROMISE/ CCPROMISE PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic DataPerform Canonical correlation between two forms of high demensional genetic data, and associate the first compoent of each form of data with a specific biologically interesting pattern of associations with multiple endpoints. A probe level analysis is also implemented.link - Attachment (Bioconductor): CCPROMISE > Perform Canonical correlation between two forms of high demensional genetic data, and associate the first compoent of each form of data with a specific biologically interesting pattern of associations with multiple endpoints. A probe level analysis is also implemented.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/fCCAC/ fCCAC functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasetsAn application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq).link - Attachment (Bioconductor): fCCAC > An application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq).

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/yarn/ yarn YARN: Robust Multi-Condition RNA-Seq Preprocessing and NormalizationExpedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.link - Attachment (Bioconductor): yarn > Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/BPRMeth/ BPRMeth Model higher-order methylation profilesBPRMeth package uses the Binomial Probit Regression likelihood to model methylation profiles and extract higher order features. These features quantitate precisely notions of shape of a methylation profile. Using these higher order features across promoter-proximal regions, we construct a powerful predictor of gene expression. Also, these features are used to cluster proximal-promoter regions using the EM algorithm.link - Attachment (Bioconductor): BPRMeth > BPRMeth package uses the Binomial Probit Regression likelihood to model methylation profiles and extract higher order features. These features quantitate precisely notions of shape of a methylation profile. Using these higher order features across promoter-proximal regions, we construct a powerful predictor of gene expression. Also, these features are used to cluster proximal-promoter regions using the EM algorithm.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/phosphonormalizer/ phosphonormalizer Compensates for the bias introduced by median normalization in phosphoproteomicsIt uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.link - Attachment (Bioconductor): phosphonormalizer (development version) > It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.link - Attachment (Bioconductor): MWASTools (development version) > MWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/GRridge/ GRridge Better prediction by use of co-data: Adaptive group-regularized ridge regressionThis package allows the use of multiple sources of co-data (e.g. external p-values, gene lists, annotation) to improve prediction of binary, continuous and survival response using (logistic, linear or Cox) group-regularized ridge regression. It also facilitates post-hoc variable selection and prediction diagnostics by cross-validation using ROC curves and AUC.link - Attachment (Bioconductor): GRridge (development version) > This package allows the use of multiple sources of co-data (e.g. external p-values, gene lists, annotation) to improve prediction of binary, continuous and survival response using (logistic, linear or Cox) group-regularized ridge regression. It also facilitates post-hoc variable selection and prediction diagnostics by cross-validation using ROC curves and AUC.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/IWTomics/ IWTomics Interval-Wise Testing for Omics DataImplementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in “Omics” data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.link - Attachment (Bioconductor): IWTomics (development version) > Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/chimeraviz/ chimeraviz Visualization tools for gene fusionschimeraviz manages data from fusion gene finders and provides useful visualization tools.link - Attachment (Bioconductor): chimeraviz (development version) > chimeraviz manages data from fusion gene finders and provides useful visualization tools.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/RnaSeqGeneEdgeRQL/ RnaSeqGeneEdgeRQL Gene-level RNA-seq differential expression and pathway analysis using Rsubread and the edgeR quasi-likelihood pipelineA workflow package for RNA-Seq experimentslink - Attachment (Bioconductor): RnaSeqGeneEdgeRQL (development version) > A workflow package for RNA-Seq experiments

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/gcapc/ gcapc GC Aware Peak CallerPeak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.link - Attachment (Bioconductor): gcapc (development version) > Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/BUMHMM/ BUMHMM Computational pipeline for computing probability of modification from structure probing experiment dataThis is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a “drop-off rate” for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of…

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/sparseDOSSA/ sparseDOSSA Sparse Data Observations for Simulating Synthetic AbundanceThe package is to provide a model based Bayesian method to characterize and simulate microbiome data. sparseDOSSA’s model captures the marginal distribution of each microbial feature as a truncated, zero-inflated log-normal distribution, with parameters distributed as a parent log-normal distribution. The model can be effectively fit to reference microbial datasets in order to parameterize their microbes and communities, or to simulate synthetic datasets of similar population structure. Most…

New Packages: Bioconductor (16:51:21): > http://bioconductor.org/packages/clusterSeq/ clusterSeq Clustering of high-throughput sequencing data by identifying co-expression patternsIdentification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.link - Attachment (Bioconductor): clusterSeq (development version) > Identification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/ramwas/ ramwas Fast Methylome-Wide Association Study Pipeline for Enrichment PlatformsRaMWAS provides a complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association…

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/scDD/ scDD Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributionsThis package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.link - Attachment (Bioconductor): scDD (development version) > This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/samExploreR/ samExploreR samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulationThis R package is designed for subsampling procedure to simulate sequencing experiments with reduced sequencing depth. This package can be used to anlayze data generated from all major sequencing platforms such as Illumina GA, HiSeq, MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM Proton sequencers. It supports multiple operating systems incluidng Linux, Mac OS X, FreeBSD and Solaris. Was developed with usage of Rsubread.link - Attachment (Bioconductor): samExploreR (development version) > This R package is designed for subsampling procedure to simulate sequencing experiments with reduced sequencing depth. This package can be used to anlayze data generated from all major sequencing platforms such as Illumina GA, HiSeq, MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM Proton sequencers. It supports multiple operating systems incluidng Linux, Mac OS X, FreeBSD and Solaris. Was developed with usage of Rsubread.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/scone/ scone Single Cell Overview of Normalized Expression dataSCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.link - Attachment (Bioconductor): scone (development version) > SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/treeio/ treeio Base Classes and Functions for Phylogenetic Tree Input and OutputBase classes and functions for parsing and exporting phylogenetic trees.link - Attachment (Bioconductor): treeio (development version) > Base classes and functions for parsing and exporting phylogenetic trees.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/RJMCMCNucleosomes/ RJMCMCNucleosomes Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.link - Attachment (Bioconductor): RJMCMCNucleosomes (development version) > This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/TCseq/ TCseq Time course sequencing data analysisQuantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of temporal patterns of time course data.link - Attachment (Bioconductor): TCseq (development version) > Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of temporal patterns of time course data.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/coseq/ coseq Co-Expression Analysis of Sequencing DataCo-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.link - Attachment (Bioconductor): coseq (development version) > Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/mimager/ mimager mimager: The Microarray ImagerEasily visualize and inspect microarrays for spatial artifacts.link - Attachment (Bioconductor): mimager (development version) > Easily visualize and inspect microarrays for spatial artifacts.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/funtooNorm/ funtooNorm Normalization Procedure for Infinium HumanMethylation450 BeadChip KitProvides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.link - Attachment (Bioconductor): funtooNorm (development version) > Provides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/DMRScan/ DMRScan Detection of Differentially Methylated RegionsThis package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The scan statistic will depend on a sequence of window sizes (# of CpGs within each window) and on a threshold for each window size. This threshold can be calculated by three different means: i) analytically using Siegmundet.al(2012) solution (preferred), ii) an important sampling as suggested by Zhang (2008), and a…

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/ChIPexoQual/ ChIPexoQual ChIPexoQualPackage with a quality control pipeline for ChIP-exo/nexus data.link - Attachment (Bioconductor): ChIPexoQual (development version) > Package with a quality control pipeline for ChIP-exo/nexus data.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/goSTAG/ goSTAG A tool to use GO Subtrees to Tag and Annotate Genes within a setGene lists derived from the results of genomic analyses are rich in biological information. For instance, differentially expressed genes (DEGs) from a microarray or RNA-Seq analysis are related functionally in terms of their response to a treatment or condition. Gene lists can vary in size, up to several thousand genes, depending on the robustness of the perturbations or how widely different the conditions are biologically. Having a way to associate biological relatedness between hundreds and…

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/splatter/ splatter Simple Simulation of Single-cell RNA Sequencing DataSplatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.link - Attachment (Bioconductor): splatter (development version) > Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/karyoploteR/ karyoploteR Plot customizable linear genomes displaying arbitrary datakaryoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.link - Attachment (Bioconductor): karyoploteR (development version) > karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/discordant/ discordant The Discordant Method: A Novel Approach for Differential CorrelationDiscordant is a method to determine differential correlation of molecular feature pairs from -omics data using mixture models. Algorithm is explained further in Siska et al.link - Attachment (Bioconductor): discordant (development version) > Discordant is a method to determine differential correlation of molecular feature pairs from -omics data using mixture models. Algorithm is explained further in Siska et al.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/POST/ POST Projection onto Orthogonal Space Testing for High Dimensional DataPerform orthogonal projection of high dimensional data of a set, and statistical modeling of phenotye with projected vectors as predictor.link - Attachment (Bioconductor): POST (development version) > Perform orthogonal projection of high dimensional data of a set, and statistical modeling of phenotye with projected vectors as predictor.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/MCbiclust/ MCbiclust Massive correlating biclusters for gene expression data and associated methodsCustom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.link - Attachment (Bioconductor): MCbiclust (development version) > Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/RTNduals/ RTNduals Analysis of co-regulatory network motifs and inference of ‘dual regulons’RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer ‘dual regulons’, a new concept that tests whether regulon pairs agree on the predicted downstream effects.link - Attachment (Bioconductor): RTNduals (development version) > RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer ‘dual regulons’, a new concept that tests whether regulon pairs agree on the predicted downstream effects.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/sampleClassifier/ sampleClassifier Sample ClassifierThe package is designed to classify gene expression profiles.link - Attachment (Bioconductor): sampleClassifier (development version) > The package is designed to classify gene expression profiles.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/geneClassifiers/ geneClassifiers Application of gene classifiersThis packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input.link - Attachment (Bioconductor): geneClassifiers (development version) > This packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input.

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/REMP/ REMP Repetitive Element Methylation PredictionMachine learing-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE. > > <a…

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/swfdr/ swfdr Science-wise false discovery rate and proportion of true null hypotheses estimationThis package allows users to estimate the science-wise false discovery rate from Jager and Leek, “Empirical estimates suggest most published medical research is true,” 2013, Biostatistics, using an EM approach due to the presence of rounding and censoring. It also allows users to estimate the proportion of true null hypotheses in the presence of covariates, using a regression framework, as per Boca and Leek, “A regression framework for the proportion of true null hypotheses,” 2015, bioRxiv…

New Packages: Bioconductor (16:51:22): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version)

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/Logolas/ Logolas Flexible and Customized Logo Plots using symbols, alphabets, numbers and alphanumeric stringsProduces logo plots of a variety of symbols and names comprising English alphabets, numerics and punctuations. Can be used for sequence motif generation, mutation pattern generation, protein amino acid geenration and symbol strength representation in any generic context.link - Attachment (Bioconductor): Logolas (development version) > Produces logo plots of a variety of symbols and names comprising English alphabets, numerics and punctuations. Can be used for sequence motif generation, mutation pattern generation, protein amino acid geenration and symbol strength representation in any generic context.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/mapscape/ mapscape mapscapeMapScape integrates clonal prevalence, clonal hierarchy, anatomic and mutational information to provide interactive visualization of spatial clonal evolution. There are four inputs to MapScape: (i) the clonal phylogeny, (ii) clonal prevalences, (iii) an image reference, which may be a medical image or drawing and (iv) pixel locations for each sample on the referenced image. Optionally, MapScape can accept a data table of mutations for each clone and their variant allele frequencies in each…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/cellscape/ cellscape Explores single cell copy number profiles in the context of a single cell treeCellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/timescape/ timescape Patient Clonal TimescapesTimeScape is an automated tool for navigating temporal clonal evolution data. The key attributes of this implementation involve the enumeration of clones, their evolutionary relationships and their shifting dynamics over time. TimeScape requires two inputs: (i) the clonal phylogeny and (ii) the clonal prevalences. Optionally, TimeScape accepts a data table of targeted mutations observed in each clone and their allele prevalences over time. The output is the TimeScape plot showing clonal…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/twoddpcr/ twoddpcr Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting moleculesThe twoddpcr package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad’s QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data. Previous work includes ‘definetherain’ (Jones et al., 2014) and ‘ddpcRquant’…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/EventPointer/ EventPointer An effective identification of alternative splicing events using junction arrays and RNA-Seq dataEventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/Organism.dplyr/ Organism.dplyr dplyr-based Access to Bioconductor Annotation ResourcesThis package provides an alternative interface to Bioconductor ‘annotation’ resources, in particular the gene identifier mapping functionality of the ‘org’ packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ‘TxDb’ packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).link - Attachment (Bioconductor): Organism.dplyr (development version) > This package provides an alternative interface to Bioconductor ‘annotation’ resources, in particular the gene identifier mapping functionality of the ‘org’ packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ‘TxDb’ packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/MIGSA/ MIGSA Massive and Integrative Gene Set AnalysisMassive and Integrative Gene Set Analysis. The MIGSA package allows to perform a massive and integrative gene set analysis over several expression and gene sets simultaneously. It provides a common gene expression analytic framework that grants a comprehensive and coherent analysis. Only a minimal user parameter setting is required to perform both singular and gene set enrichment analyses in an integrative manner by means of the best available methods, i.e. dEnricher and…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/rqt/ rqt rqt: utilities for gene-level meta-analysisDespite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: “Gene-set association tests for next-generation sequencing data” by Lee et al (2016), Bioinformatics, 32(17), i611-i619,http://bioconductor.org/packages/rqt/ - Attachment (Bioconductor): rqt (development version) > Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see:

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/GISPA/ GISPA GISPA: Method for Gene Integrated Set Profile AnalysisGISPA is a method intended for the researchers who are interested in defining gene sets with similar, a priori specified molecular profile. GISPA method has been previously published in Nucleic Acid Research (Kowalski et al., 2016; PMID: 26826710).link - Attachment (Bioconductor): GISPA (development version) > GISPA is a method intended for the researchers who are interested in defining gene sets with similar, a priori specified molecular profile. GISPA method has been previously published in Nucleic Acid Research (Kowalski et al., 2016; PMID: 26826710).

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/hicrep/ hicrep Measuring the reproducibility of Hi-C dataHi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance-dependence. We present a novel reproducibility measure that systematically takes these features into consideration. This measure can assess pairwise differences between Hi-C matrices under a wide range of settings, and can be used to…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/epiNEM/ epiNEM epiNEMepiNEM is an extension of the original Nested Effects Models (NEM). EpiNEM is able to take into account double knockouts and infer more complex network signalling pathways.link - Attachment (Bioconductor): epiNEM (development version) > epiNEM is an extension of the original Nested Effects Models (NEM). EpiNEM is able to take into account double knockouts and infer more complex network signalling pathways.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/IntEREst/ IntEREst Intron-Exon Retention EstimatorThis package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).link - Attachment (Bioconductor): IntEREst (development version) > This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/pathprint/ pathprint Pathway fingerprinting for analysis of gene expression arraysAlgorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.link - Attachment (Bioconductor): pathprint (development version) > Algorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/multiOmicsViz/ multiOmicsViz Plot the effect of one omics data on other omics data along the chromosomeCalculate the spearman correlation between the source omics data and other target omics data, identify the significant correlations and plot the significant correlations on the heat map in which the x-axis and y-axis are ordered by the chromosomal location.link - Attachment (Bioconductor): multiOmicsViz (development version) > Calculate the spearman correlation between the source omics data and other target omics data, identify the significant correlations and plot the significant correlations on the heat map in which the x-axis and y-axis are ordered by the chromosomal location.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/MaxContrastProjection/ MaxContrastProjection Perform a maximum contrast projection of 3D images along the z-dimension into 2DA problem when recording 3D fluorescent microscopy images is how to properly present these results in 2D. Maximum intensity projections are a popular method to determine the focal plane of each pixel in the image. The problem with this approach, however, is that out-of-focus elements will still be visible, making edges and fine structures difficult to detect. This package aims to resolve this problem by using the contrast around a given pixel to determine the focal plane, allowing for a much…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/branchpointer/ branchpointer Prediction of intronic splicing branchpointsPredicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.link - Attachment (Bioconductor): branchpointer (development version) > Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/DaMiRseq/ DaMiRseq Data Mining for RNA-seq data: normalization, feature selection and classificationThe DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them for classification purposes.. The package accepts any kind of data presented as a table of raw counts and allows including covariates that occur with the experimental setting. A series of functions enable the user to clean up the data by filtering genomic features and samples, to adjust data by identifying and removing the unwanted source of variation (i.e….

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/BioCor/ BioCor Functional similaritiesCalculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships…link - Attachment (Bioconductor): BioCor (development version) > Calculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache (development version) > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/motifcounter/ motifcounter R package for analysing TFBSs in DNA sequences‘motifcounter’ provides functionality to compute the statistics related with motif matching and counting of motif matches in DNA sequences. As an input, ‘motifcounter’ requires a motif in terms of a position frequency matrix (PFM). Furthermore, a set of DNA sequences is required to estimated a higher-order background model (BGM). The package provides functions to investigate the the per-position and per strand log-likelihood scores between the PFM and the BGM across a given sequence of set of…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/cydar/ cydar Using Mass Cytometry for Differential Abundance AnalysesIdentifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.link - Attachment (Bioconductor): cydar (development version) > Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/netReg/ netReg Network-Regularized Regression ModelsnetReg fits linear regression models using network-penalization. Graph prior knowledge, in the form of biological networks, is being incorporated into the likelihood of the linear model. The networks describe biological relationships such as co-regulation or dependency of the same transcription factors/metabolites/etc. yielding a part sparse and part smooth solution for coefficient profiles.link - Attachment (Bioconductor): netReg (development version) > netReg fits linear regression models using network-penalization. Graph prior knowledge, in the form of biological networks, is being incorporated into the likelihood of the linear model. The networks describe biological relationships such as co-regulation or dependency of the same transcription factors/metabolites/etc. yielding a part sparse and part smooth solution for coefficient profiles.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/GA4GHclient/ GA4GHclient A Bioconductor package for accessing GA4GH API data serversGA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.link - Attachment (Bioconductor): GA4GHclient (development version) > GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/STROMA4/ STROMA4 Assign Properties to TNBC PatientsThis package estimates four stromal properties identified in TNBC patients in each patient of a gene expression datasets. These stromal property assignments can be combined to subtype patients. These four stromal properties were identified in Triple negative breast cancer (TNBC) patients and represent the presence of different cells in the stroma: T-cells (T), B-cells (B), stromal infiltrating epithelial cells (E), and desmoplasia (D). Additionally this package can also be used to estimate…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/flowTime/ flowTime Annotation and analysis of biological dynamical systems using flow cytometryThis package was developed for analysis of both dynamic and steady state experiments examining the function of gene regulatory networks in yeast (strain W303) expressing fluorescent reporter proteins using a BD Accuri C6 and SORP cytometers. However, the functions are for the most part general and may be adapted for analysis of other organisms using other flow cytometers. Functions in this package facilitate the annotation of flow cytometry data with experimental metadata, as is requisite for…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/wiggleplotr/ wiggleplotr Make read coverage plots from BigWig filesTools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.link - Attachment (Bioconductor): wiggleplotr (development version) > Tools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/AnnotationFilter/ AnnotationFilter Facilities for Filtering Bioconductor Annotation ResourcesThis package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.link - Attachment (Bioconductor): AnnotationFilter (development version) > This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/NADfinder/ NADfinder Call wide peaks for sequencing dataCall peaks for two samples: target and control. It will count the reads for tiles of the genome and then convert it to ratios. The ratios will be corrected and smoothed. The z-scores is calculated for each counting windows over the background. The peaks will be detected based on z-scores.link - Attachment (Bioconductor): NADfinder (development version) > Call peaks for two samples: target and control. It will count the reads for tiles of the genome and then convert it to ratios. The ratios will be corrected and smoothed. The z-scores is calculated for each counting windows over the background. The peaks will be detected based on z-scores.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/GenomicDataCommons/ GenomicDataCommons NIH / NCI Genomic Data Commons AccessProgrammatically access the NIH / NCI Genomic Data Commons RESTful service.link - Attachment (Bioconductor): GenomicDataCommons (development version) > Programmatically access the NIH / NCI Genomic Data Commons RESTful service.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/RIVER/ RIVER R package for RIVER (RNA-Informed Variant Effect on Regulation)An implementation of a probabilistic modeling framework that jointly analyzes personal genome and transcriptome data to estimate the probability that a variant has regulatory impact in that individual. It is based on a generative model that assumes that genomic annotations, such as the location of a variant with respect to regulatory elements, determine the prior probability that variant is a functional regulatory variant, which is an unobserved variable. The functional regulatory variant…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/BioMedR/ BioMedR Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their InteractionsThe BioMedR package offers an R/Bioconductor package generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions.link - Attachment (Bioconductor): BioMedR (development version) > The BioMedR package offers an R/Bioconductor package generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/banocc/ banocc Bayesian ANalysis Of Compositional CovarianceBAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded withrstan. It provides as output thestanfitobject as well as posterior median and credible interval estimates for each correlation element.link - Attachment (Bioconductor): banocc (development version) > BAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded with rstan. It provides as output the stanfit object as well as posterior median and credible interval estimates for each correlation element.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/RaggedExperiment/ RaggedExperiment Representation of Sparse Experiments and Assays Across SamplesThis package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns.link - Attachment (Bioconductor): RaggedExperiment (development version) > This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/basecallQC/ basecallQC Working with Illumina Basecalling and Demultiplexing input and output filesThe basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions = 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/CATALYST/ CATALYST Cytometry dATa anALYSis ToolsMass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores (development version) > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/IMAS/ IMAS Integrative analysis of Multi-omics data for Alternative SplicingIntegrative analysis of Multi-omics data for Alternative splicing.link - Attachment (Bioconductor): IMAS (development version) > Integrative analysis of Multi-omics data for Alternative splicing.

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/semisup/ semisup Detecting SNPs with interactive effects on a quantitative traitThis R packages moves away from testing interaction terms, and move towards testing whether an individual SNP is involved in any interaction. This reduces the multiple testing burden to one test per SNP, and allows for interactions with unobserved factors. Analysing one SNP at a time, it splits the individuals into two groups, based on the number of minor alleles. If the quantitative trait differs in mean between the two groups, the SNP has a main effect. If the quantitative trait differs in…

New Packages: Bioconductor (16:51:23): > http://bioconductor.org/packages/ImpulseDE2/ ImpulseDE2 Differential expression analysis of longitudinal count data setsImpulseDE2 is a differential expression algorithm for longitudinal count data sets which arise in sequencing experiments such as RNA-seq, ChIP-seq, ATAC-seq and DNaseI-seq. ImpulseDE2 is based on a negative binomial noise model with dispersion trend smoothing by DESeq2 and uses the impulse model to constrain the mean expression trajectory of each gene. The impulse model was empirically found to fit global expression changes in cells after environmental and developmental stimuli and is…

New Packages: Bioconductor (16:51:24): > http://bioconductor.org/packages/methylInheritance/ methylInheritance Permutation-Based Analysis associating Conserved Differentially Methylated Elements from One Generation to the Next to a Treatment EffectPermutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.link - Attachment (Bioconductor): methylInheritance (development version) > Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.

New Packages: Bioconductor (16:51:24): > http://bioconductor.org/packages/biotmle/ biotmle Targeted Learning for Biomarker Discovery with Moderated StatisticsThis package facilitates the discovery of biomarkers from biological sequencing data (e.g., microarrays, RNA-seq) based on the associations of potential biomarkers with exposure and outcome variables by implementing an estimation procedure that combines a generalization of the moderated t-statistic with asymptotically linear statistical parameters estimated via targeted minimum loss-based estimation (TMLE).link - Attachment (Bioconductor): biotmle (development version) > This package facilitates the discovery of biomarkers from biological sequencing data (e.g., microarrays, RNA-seq) based on the associations of potential biomarkers with exposure and outcome variables by implementing an estimation procedure that combines a generalization of the moderated t-statistic with asymptotically linear statistical parameters estimated via targeted minimum loss-based estimation (TMLE).

New Packages: Bioconductor (16:51:24): > http://bioconductor.org/packages/BLMA/ BLMA BLMA: A package for bi-level meta-analysisSuit of tools for bi-level meta-analysis. The package can be used in a wide range of applications, including general hypothesis testings, differential expression analysis, functional analysis, and pathway analysis.link - Attachment (Bioconductor): BLMA (development version) > Suit of tools for bi-level meta-analysis. The package can be used in a wide range of applications, including general hypothesis testings, differential expression analysis, functional analysis, and pathway analysis.

New Packages: Bioconductor (16:51:24): > http://bioconductor.org/packages/metavizr/ metavizr R Interface to the metaviz web app for interactive metagenomics data analysis and visualizationThis package provides Websocket communication to the metaviz web app (http://metaviz.cbcb.umd.edu) for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported (e.g., MRexperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as… - Attachment (metaviz.cbcb.umd.edu): Metaviz > Epiviz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

New Packages: Bioconductor (16:51:24): > http://bioconductor.org/packages/cellbaseR/ cellbaseR Querying annotation data from the high performance Cellbase web servicesThis R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.link - Attachment (Bioconductor): cellbaseR (development version) > This R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.

New Packages: Bioconductor (16:51:24): > http://bioconductor.org/packages/PPInfer/ PPInfer Inferring functionally related proteins using protein interaction networksInteractions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn urshered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at…

New Packages: Bioconductor (16:51:24): > http://bioconductor.org/packages/ideal/ ideal Interactive Differential Expression AnaLysisThis package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package.link - Attachment (Bioconductor): ideal (development version) > This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package.

New Packages: Bioconductor (21:06:24): > http://bioconductor.org/packages/psichomics/ psichomics Graphical Interface for Alternative Splicing Quantification, Analysis and VisualisationInteractive R package with a Shiny-based graphical interface for the quantification, analysis and visualisation of alternative splicing data from The Cancer Genome Atlas (TCGA) or the Genotype-Tissue Expression (GTEx) project. This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA and GTEx samples. > > <a…

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/MutationalPatterns/ MutationalPatterns Studying patterns in base substitution cataloguesAn extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.link - Attachment (Bioconductor): MutationalPatterns > An extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/HelloRanges/ HelloRanges Introduce *Ranges to bedtools usersTranslates bedtools command-line invocations to R code calling functions from the Bioconductor Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.link - Attachment (Bioconductor): HelloRanges > Translates bedtools command-line invocations to R code calling functions from the Bioconductor Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/crisprseekplus/ crisprseekplus crisprseekplusBioinformatics platform containing interface to work with offTargetAnalysis and compare2Sequences in the CRISPRseek package, and GUIDEseqAnalysis.link - Attachment (Bioconductor): crisprseekplus > Bioinformatics platform containing interface to work with offTargetAnalysis and compare2Sequences in the CRISPRseek package, and GUIDEseqAnalysis.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/meshes/ meshes MeSH Enrichment and Semantic analysesMeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide…

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/M3Drop/ M3Drop Michaelis-Menten Modelling of Dropouts in single-cell RNASeqThis package fits a Michaelis-Menten model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells.link - Attachment (Bioconductor): M3Drop > This package fits a Michaelis-Menten model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/TVTB/ TVTB TVTB: The VCF Tool BoxThe package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).link - Attachment (Bioconductor): TVTB > The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/StarBioTrek/ StarBioTrek StarBioTrekThis tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.link - Attachment (Bioconductor): StarBioTrek > This tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/regsplice/ regsplice L1-regularization based methods for detection of differential splicingStatistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.link - Attachment (Bioconductor): regsplice > Statistical methods for detection of differential exon usage in RNA-seq and exon microarray data sets, using L1 regularization (lasso) to improve power.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/yamss/ yamss Tools for high-throughput metabolomicsTools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.link - Attachment (Bioconductor): yamss > Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/proFIA/ proFIA Preprocessing of FIA-HRMS dataFlow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and…

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/CCPROMISE/ CCPROMISE PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic DataPerform Canonical correlation between two forms of high demensional genetic data, and associate the first compoent of each form of data with a specific biologically interesting pattern of associations with multiple endpoints. A probe level analysis is also implemented.link - Attachment (Bioconductor): CCPROMISE > Perform Canonical correlation between two forms of high demensional genetic data, and associate the first compoent of each form of data with a specific biologically interesting pattern of associations with multiple endpoints. A probe level analysis is also implemented.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/fCCAC/ fCCAC functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasetsAn application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq).link - Attachment (Bioconductor): fCCAC > An application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq).

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/yarn/ yarn YARN: Robust Multi-Condition RNA-Seq Preprocessing and NormalizationExpedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.link - Attachment (Bioconductor): yarn > Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/BPRMeth/ BPRMeth Model higher-order methylation profilesBPRMeth package uses the Binomial Probit Regression likelihood to model methylation profiles and extract higher order features. These features quantitate precisely notions of shape of a methylation profile. Using these higher order features across promoter-proximal regions, we construct a powerful predictor of gene expression. Also, these features are used to cluster proximal-promoter regions using the EM algorithm.link - Attachment (Bioconductor): BPRMeth > BPRMeth package uses the Binomial Probit Regression likelihood to model methylation profiles and extract higher order features. These features quantitate precisely notions of shape of a methylation profile. Using these higher order features across promoter-proximal regions, we construct a powerful predictor of gene expression. Also, these features are used to cluster proximal-promoter regions using the EM algorithm.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/phosphonormalizer/ phosphonormalizer Compensates for the bias introduced by median normalization in phosphoproteomicsIt uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.link - Attachment (Bioconductor): phosphonormalizer (development version) > It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.link - Attachment (Bioconductor): MWASTools (development version) > MWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/GRridge/ GRridge Better prediction by use of co-data: Adaptive group-regularized ridge regressionThis package allows the use of multiple sources of co-data (e.g. external p-values, gene lists, annotation) to improve prediction of binary, continuous and survival response using (logistic, linear or Cox) group-regularized ridge regression. It also facilitates post-hoc variable selection and prediction diagnostics by cross-validation using ROC curves and AUC.link - Attachment (Bioconductor): GRridge (development version) > This package allows the use of multiple sources of co-data (e.g. external p-values, gene lists, annotation) to improve prediction of binary, continuous and survival response using (logistic, linear or Cox) group-regularized ridge regression. It also facilitates post-hoc variable selection and prediction diagnostics by cross-validation using ROC curves and AUC.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/IWTomics/ IWTomics Interval-Wise Testing for Omics DataImplementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in “Omics” data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.link - Attachment (Bioconductor): IWTomics (development version) > Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/chimeraviz/ chimeraviz Visualization tools for gene fusionschimeraviz manages data from fusion gene finders and provides useful visualization tools.link - Attachment (Bioconductor): chimeraviz (development version) > chimeraviz manages data from fusion gene finders and provides useful visualization tools.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/RnaSeqGeneEdgeRQL/ RnaSeqGeneEdgeRQL Gene-level RNA-seq differential expression and pathway analysis using Rsubread and the edgeR quasi-likelihood pipelineA workflow package for RNA-Seq experimentslink - Attachment (Bioconductor): RnaSeqGeneEdgeRQL (development version) > A workflow package for RNA-Seq experiments

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/gcapc/ gcapc GC Aware Peak CallerPeak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.link - Attachment (Bioconductor): gcapc (development version) > Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/BUMHMM/ BUMHMM Computational pipeline for computing probability of modification from structure probing experiment dataThis is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a “drop-off rate” for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of…

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/sparseDOSSA/ sparseDOSSA Sparse Data Observations for Simulating Synthetic AbundanceThe package is to provide a model based Bayesian method to characterize and simulate microbiome data. sparseDOSSA’s model captures the marginal distribution of each microbial feature as a truncated, zero-inflated log-normal distribution, with parameters distributed as a parent log-normal distribution. The model can be effectively fit to reference microbial datasets in order to parameterize their microbes and communities, or to simulate synthetic datasets of similar population structure. Most…

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/clusterSeq/ clusterSeq Clustering of high-throughput sequencing data by identifying co-expression patternsIdentification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.link - Attachment (Bioconductor): clusterSeq (development version) > Identification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/ramwas/ ramwas Fast Methylome-Wide Association Study Pipeline for Enrichment PlatformsRaMWAS provides a complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association…

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/scDD/ scDD Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributionsThis package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.link - Attachment (Bioconductor): scDD (development version) > This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/samExploreR/ samExploreR samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulationThis R package is designed for subsampling procedure to simulate sequencing experiments with reduced sequencing depth. This package can be used to anlayze data generated from all major sequencing platforms such as Illumina GA, HiSeq, MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM Proton sequencers. It supports multiple operating systems incluidng Linux, Mac OS X, FreeBSD and Solaris. Was developed with usage of Rsubread.link - Attachment (Bioconductor): samExploreR (development version) > This R package is designed for subsampling procedure to simulate sequencing experiments with reduced sequencing depth. This package can be used to anlayze data generated from all major sequencing platforms such as Illumina GA, HiSeq, MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM Proton sequencers. It supports multiple operating systems incluidng Linux, Mac OS X, FreeBSD and Solaris. Was developed with usage of Rsubread.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/scone/ scone Single Cell Overview of Normalized Expression dataSCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.link - Attachment (Bioconductor): scone (development version) > SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.

New Packages: Bioconductor (21:06:25): > http://bioconductor.org/packages/treeio/ treeio Base Classes and Functions for Phylogenetic Tree Input and OutputBase classes and functions for parsing and exporting phylogenetic trees.link - Attachment (Bioconductor): treeio (development version) > Base classes and functions for parsing and exporting phylogenetic trees.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/RJMCMCNucleosomes/ RJMCMCNucleosomes Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.link - Attachment (Bioconductor): RJMCMCNucleosomes (development version) > This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/TCseq/ TCseq Time course sequencing data analysisQuantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of temporal patterns of time course data.link - Attachment (Bioconductor): TCseq (development version) > Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of temporal patterns of time course data.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/coseq/ coseq Co-Expression Analysis of Sequencing DataCo-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.link - Attachment (Bioconductor): coseq (development version) > Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/mimager/ mimager mimager: The Microarray ImagerEasily visualize and inspect microarrays for spatial artifacts.link - Attachment (Bioconductor): mimager (development version) > Easily visualize and inspect microarrays for spatial artifacts.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/funtooNorm/ funtooNorm Normalization Procedure for Infinium HumanMethylation450 BeadChip KitProvides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.link - Attachment (Bioconductor): funtooNorm (development version) > Provides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/DMRScan/ DMRScan Detection of Differentially Methylated RegionsThis package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The scan statistic will depend on a sequence of window sizes (# of CpGs within each window) and on a threshold for each window size. This threshold can be calculated by three different means: i) analytically using Siegmundet.al(2012) solution (preferred), ii) an important sampling as suggested by Zhang (2008), and a…

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/ChIPexoQual/ ChIPexoQual ChIPexoQualPackage with a quality control pipeline for ChIP-exo/nexus data.link - Attachment (Bioconductor): ChIPexoQual (development version) > Package with a quality control pipeline for ChIP-exo/nexus data.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/goSTAG/ goSTAG A tool to use GO Subtrees to Tag and Annotate Genes within a setGene lists derived from the results of genomic analyses are rich in biological information. For instance, differentially expressed genes (DEGs) from a microarray or RNA-Seq analysis are related functionally in terms of their response to a treatment or condition. Gene lists can vary in size, up to several thousand genes, depending on the robustness of the perturbations or how widely different the conditions are biologically. Having a way to associate biological relatedness between hundreds and…

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/splatter/ splatter Simple Simulation of Single-cell RNA Sequencing DataSplatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.link - Attachment (Bioconductor): splatter (development version) > Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/karyoploteR/ karyoploteR Plot customizable linear genomes displaying arbitrary datakaryoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.link - Attachment (Bioconductor): karyoploteR (development version) > karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/discordant/ discordant The Discordant Method: A Novel Approach for Differential CorrelationDiscordant is a method to determine differential correlation of molecular feature pairs from -omics data using mixture models. Algorithm is explained further in Siska et al.link - Attachment (Bioconductor): discordant (development version) > Discordant is a method to determine differential correlation of molecular feature pairs from -omics data using mixture models. Algorithm is explained further in Siska et al.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/POST/ POST Projection onto Orthogonal Space Testing for High Dimensional DataPerform orthogonal projection of high dimensional data of a set, and statistical modeling of phenotye with projected vectors as predictor.link - Attachment (Bioconductor): POST (development version) > Perform orthogonal projection of high dimensional data of a set, and statistical modeling of phenotye with projected vectors as predictor.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/MCbiclust/ MCbiclust Massive correlating biclusters for gene expression data and associated methodsCustom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.link - Attachment (Bioconductor): MCbiclust (development version) > Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/RTNduals/ RTNduals Analysis of co-regulatory network motifs and inference of ‘dual regulons’RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer ‘dual regulons’, a new concept that tests whether regulon pairs agree on the predicted downstream effects.link - Attachment (Bioconductor): RTNduals (development version) > RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer ‘dual regulons’, a new concept that tests whether regulon pairs agree on the predicted downstream effects.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/sampleClassifier/ sampleClassifier Sample ClassifierThe package is designed to classify gene expression profiles.link - Attachment (Bioconductor): sampleClassifier (development version) > The package is designed to classify gene expression profiles.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/geneClassifiers/ geneClassifiers Application of gene classifiersThis packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input.link - Attachment (Bioconductor): geneClassifiers (development version) > This packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/REMP/ REMP Repetitive Element Methylation PredictionMachine learing-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE. > > <a…

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/swfdr/ swfdr Science-wise false discovery rate and proportion of true null hypotheses estimationThis package allows users to estimate the science-wise false discovery rate from Jager and Leek, “Empirical estimates suggest most published medical research is true,” 2013, Biostatistics, using an EM approach due to the presence of rounding and censoring. It also allows users to estimate the proportion of true null hypotheses in the presence of covariates, using a regression framework, as per Boca and Leek, “A regression framework for the proportion of true null hypotheses,” 2015, bioRxiv…

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI (development version)

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/Logolas/ Logolas Flexible and Customized Logo Plots using symbols, alphabets, numbers and alphanumeric stringsProduces logo plots of a variety of symbols and names comprising English alphabets, numerics and punctuations. Can be used for sequence motif generation, mutation pattern generation, protein amino acid geenration and symbol strength representation in any generic context.link - Attachment (Bioconductor): Logolas (development version) > Produces logo plots of a variety of symbols and names comprising English alphabets, numerics and punctuations. Can be used for sequence motif generation, mutation pattern generation, protein amino acid geenration and symbol strength representation in any generic context.

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/mapscape/ mapscape mapscapeMapScape integrates clonal prevalence, clonal hierarchy, anatomic and mutational information to provide interactive visualization of spatial clonal evolution. There are four inputs to MapScape: (i) the clonal phylogeny, (ii) clonal prevalences, (iii) an image reference, which may be a medical image or drawing and (iv) pixel locations for each sample on the referenced image. Optionally, MapScape can accept a data table of mutations for each clone and their variant allele frequencies in each…

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/cellscape/ cellscape Explores single cell copy number profiles in the context of a single cell treeCellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of…

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/timescape/ timescape Patient Clonal TimescapesTimeScape is an automated tool for navigating temporal clonal evolution data. The key attributes of this implementation involve the enumeration of clones, their evolutionary relationships and their shifting dynamics over time. TimeScape requires two inputs: (i) the clonal phylogeny and (ii) the clonal prevalences. Optionally, TimeScape accepts a data table of targeted mutations observed in each clone and their allele prevalences over time. The output is the TimeScape plot showing clonal…

New Packages: Bioconductor (21:06:26): > http://bioconductor.org/packages/twoddpcr/ twoddpcr Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting moleculesThe twoddpcr package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad’s QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data. Previous work includes ‘definetherain’ (Jones et al., 2014) and ‘ddpcRquant’…

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/EventPointer/ EventPointer An effective identification of alternative splicing events using junction arrays and RNA-Seq dataEventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative…

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/Organism.dplyr/ Organism.dplyr dplyr-based Access to Bioconductor Annotation ResourcesThis package provides an alternative interface to Bioconductor ‘annotation’ resources, in particular the gene identifier mapping functionality of the ‘org’ packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ‘TxDb’ packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).link - Attachment (Bioconductor): Organism.dplyr (development version) > This package provides an alternative interface to Bioconductor ‘annotation’ resources, in particular the gene identifier mapping functionality of the ‘org’ packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ‘TxDb’ packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/MIGSA/ MIGSA Massive and Integrative Gene Set AnalysisMassive and Integrative Gene Set Analysis. The MIGSA package allows to perform a massive and integrative gene set analysis over several expression and gene sets simultaneously. It provides a common gene expression analytic framework that grants a comprehensive and coherent analysis. Only a minimal user parameter setting is required to perform both singular and gene set enrichment analyses in an integrative manner by means of the best available methods, i.e. dEnricher and…

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/rqt/ rqt rqt: utilities for gene-level meta-analysisDespite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: “Gene-set association tests for next-generation sequencing data” by Lee et al (2016), Bioinformatics, 32(17), i611-i619,http://bioconductor.org/packages/rqt/ - Attachment (Bioconductor): rqt (development version) > Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see:

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/GISPA/ GISPA GISPA: Method for Gene Integrated Set Profile AnalysisGISPA is a method intended for the researchers who are interested in defining gene sets with similar, a priori specified molecular profile. GISPA method has been previously published in Nucleic Acid Research (Kowalski et al., 2016; PMID: 26826710).link - Attachment (Bioconductor): GISPA (development version) > GISPA is a method intended for the researchers who are interested in defining gene sets with similar, a priori specified molecular profile. GISPA method has been previously published in Nucleic Acid Research (Kowalski et al., 2016; PMID: 26826710).

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/hicrep/ hicrep Measuring the reproducibility of Hi-C dataHi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance-dependence. We present a novel reproducibility measure that systematically takes these features into consideration. This measure can assess pairwise differences between Hi-C matrices under a wide range of settings, and can be used to…

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/epiNEM/ epiNEM epiNEMepiNEM is an extension of the original Nested Effects Models (NEM). EpiNEM is able to take into account double knockouts and infer more complex network signalling pathways.link - Attachment (Bioconductor): epiNEM (development version) > epiNEM is an extension of the original Nested Effects Models (NEM). EpiNEM is able to take into account double knockouts and infer more complex network signalling pathways.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/IntEREst/ IntEREst Intron-Exon Retention EstimatorThis package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).link - Attachment (Bioconductor): IntEREst (development version) > This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/pathprint/ pathprint Pathway fingerprinting for analysis of gene expression arraysAlgorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.link - Attachment (Bioconductor): pathprint (development version) > Algorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/multiOmicsViz/ multiOmicsViz Plot the effect of one omics data on other omics data along the chromosomeCalculate the spearman correlation between the source omics data and other target omics data, identify the significant correlations and plot the significant correlations on the heat map in which the x-axis and y-axis are ordered by the chromosomal location.link - Attachment (Bioconductor): multiOmicsViz (development version) > Calculate the spearman correlation between the source omics data and other target omics data, identify the significant correlations and plot the significant correlations on the heat map in which the x-axis and y-axis are ordered by the chromosomal location.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/MaxContrastProjection/ MaxContrastProjection Perform a maximum contrast projection of 3D images along the z-dimension into 2DA problem when recording 3D fluorescent microscopy images is how to properly present these results in 2D. Maximum intensity projections are a popular method to determine the focal plane of each pixel in the image. The problem with this approach, however, is that out-of-focus elements will still be visible, making edges and fine structures difficult to detect. This package aims to resolve this problem by using the contrast around a given pixel to determine the focal plane, allowing for a much…

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/branchpointer/ branchpointer Prediction of intronic splicing branchpointsPredicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.link - Attachment (Bioconductor): branchpointer (development version) > Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/DaMiRseq/ DaMiRseq Data Mining for RNA-seq data: normalization, feature selection and classificationThe DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them for classification purposes.. The package accepts any kind of data presented as a table of raw counts and allows including covariates that occur with the experimental setting. A series of functions enable the user to clean up the data by filtering genomic features and samples, to adjust data by identifying and removing the unwanted source of variation (i.e….

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/BioCor/ BioCor Functional similaritiesCalculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships…link - Attachment (Bioconductor): BioCor (development version) > Calculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships…

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache (development version) > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/motifcounter/ motifcounter R package for analysing TFBSs in DNA sequences‘motifcounter’ provides functionality to compute the statistics related with motif matching and counting of motif matches in DNA sequences. As an input, ‘motifcounter’ requires a motif in terms of a position frequency matrix (PFM). Furthermore, a set of DNA sequences is required to estimated a higher-order background model (BGM). The package provides functions to investigate the the per-position and per strand log-likelihood scores between the PFM and the BGM across a given sequence of set of…

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/cydar/ cydar Using Mass Cytometry for Differential Abundance AnalysesIdentifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.link - Attachment (Bioconductor): cydar (development version) > Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/netReg/ netReg Network-Regularized Regression ModelsnetReg fits linear regression models using network-penalization. Graph prior knowledge, in the form of biological networks, is being incorporated into the likelihood of the linear model. The networks describe biological relationships such as co-regulation or dependency of the same transcription factors/metabolites/etc. yielding a part sparse and part smooth solution for coefficient profiles.link - Attachment (Bioconductor): netReg (development version) > netReg fits linear regression models using network-penalization. Graph prior knowledge, in the form of biological networks, is being incorporated into the likelihood of the linear model. The networks describe biological relationships such as co-regulation or dependency of the same transcription factors/metabolites/etc. yielding a part sparse and part smooth solution for coefficient profiles.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/GA4GHclient/ GA4GHclient A Bioconductor package for accessing GA4GH API data serversGA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.link - Attachment (Bioconductor): GA4GHclient (development version) > GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/STROMA4/ STROMA4 Assign Properties to TNBC PatientsThis package estimates four stromal properties identified in TNBC patients in each patient of a gene expression datasets. These stromal property assignments can be combined to subtype patients. These four stromal properties were identified in Triple negative breast cancer (TNBC) patients and represent the presence of different cells in the stroma: T-cells (T), B-cells (B), stromal infiltrating epithelial cells (E), and desmoplasia (D). Additionally this package can also be used to estimate…

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/flowTime/ flowTime Annotation and analysis of biological dynamical systems using flow cytometryThis package was developed for analysis of both dynamic and steady state experiments examining the function of gene regulatory networks in yeast (strain W303) expressing fluorescent reporter proteins using a BD Accuri C6 and SORP cytometers. However, the functions are for the most part general and may be adapted for analysis of other organisms using other flow cytometers. Functions in this package facilitate the annotation of flow cytometry data with experimental metadata, as is requisite for…

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/wiggleplotr/ wiggleplotr Make read coverage plots from BigWig filesTools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.link - Attachment (Bioconductor): wiggleplotr (development version) > Tools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/AnnotationFilter/ AnnotationFilter Facilities for Filtering Bioconductor Annotation ResourcesThis package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.link - Attachment (Bioconductor): AnnotationFilter (development version) > This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/NADfinder/ NADfinder Call wide peaks for sequencing dataCall peaks for two samples: target and control. It will count the reads for tiles of the genome and then convert it to ratios. The ratios will be corrected and smoothed. The z-scores is calculated for each counting windows over the background. The peaks will be detected based on z-scores.link - Attachment (Bioconductor): NADfinder (development version) > Call peaks for two samples: target and control. It will count the reads for tiles of the genome and then convert it to ratios. The ratios will be corrected and smoothed. The z-scores is calculated for each counting windows over the background. The peaks will be detected based on z-scores.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/GenomicDataCommons/ GenomicDataCommons NIH / NCI Genomic Data Commons AccessProgrammatically access the NIH / NCI Genomic Data Commons RESTful service.link - Attachment (Bioconductor): GenomicDataCommons (development version) > Programmatically access the NIH / NCI Genomic Data Commons RESTful service.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/RIVER/ RIVER R package for RIVER (RNA-Informed Variant Effect on Regulation)An implementation of a probabilistic modeling framework that jointly analyzes personal genome and transcriptome data to estimate the probability that a variant has regulatory impact in that individual. It is based on a generative model that assumes that genomic annotations, such as the location of a variant with respect to regulatory elements, determine the prior probability that variant is a functional regulatory variant, which is an unobserved variable. The functional regulatory variant…

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/BioMedR/ BioMedR Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their InteractionsThe BioMedR package offers an R/Bioconductor package generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions.link - Attachment (Bioconductor): BioMedR (development version) > The BioMedR package offers an R/Bioconductor package generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/banocc/ banocc Bayesian ANalysis Of Compositional CovarianceBAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded withrstan. It provides as output thestanfitobject as well as posterior median and credible interval estimates for each correlation element.link - Attachment (Bioconductor): banocc (development version) > BAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded with rstan. It provides as output the stanfit object as well as posterior median and credible interval estimates for each correlation element.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/RaggedExperiment/ RaggedExperiment Representation of Sparse Experiments and Assays Across SamplesThis package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns.link - Attachment (Bioconductor): RaggedExperiment (development version) > This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns.

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/basecallQC/ basecallQC Working with Illumina Basecalling and Demultiplexing input and output filesThe basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions = 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages…

New Packages: Bioconductor (21:06:27): > http://bioconductor.org/packages/CATALYST/ CATALYST Cytometry dATa anALYSis ToolsMass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to…

New Packages: Bioconductor (21:06:28): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores (development version) > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

New Packages: Bioconductor (21:06:28): > http://bioconductor.org/packages/IMAS/ IMAS Integrative analysis of Multi-omics data for Alternative SplicingIntegrative analysis of Multi-omics data for Alternative splicing.link - Attachment (Bioconductor): IMAS (development version) > Integrative analysis of Multi-omics data for Alternative splicing.

New Packages: Bioconductor (21:06:28): > http://bioconductor.org/packages/semisup/ semisup Detecting SNPs with interactive effects on a quantitative traitThis R packages moves away from testing interaction terms, and move towards testing whether an individual SNP is involved in any interaction. This reduces the multiple testing burden to one test per SNP, and allows for interactions with unobserved factors. Analysing one SNP at a time, it splits the individuals into two groups, based on the number of minor alleles. If the quantitative trait differs in mean between the two groups, the SNP has a main effect. If the quantitative trait differs in…

New Packages: Bioconductor (21:06:28): > http://bioconductor.org/packages/ImpulseDE2/ ImpulseDE2 Differential expression analysis of longitudinal count data setsImpulseDE2 is a differential expression algorithm for longitudinal count data sets which arise in sequencing experiments such as RNA-seq, ChIP-seq, ATAC-seq and DNaseI-seq. ImpulseDE2 is based on a negative binomial noise model with dispersion trend smoothing by DESeq2 and uses the impulse model to constrain the mean expression trajectory of each gene. The impulse model was empirically found to fit global expression changes in cells after environmental and developmental stimuli and is…

New Packages: Bioconductor (21:06:28): > http://bioconductor.org/packages/methylInheritance/ methylInheritance Permutation-Based Analysis associating Conserved Differentially Methylated Elements from One Generation to the Next to a Treatment EffectPermutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.link - Attachment (Bioconductor): methylInheritance (development version) > Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.

New Packages: Bioconductor (21:06:28): > http://bioconductor.org/packages/biotmle/ biotmle Targeted Learning for Biomarker Discovery with Moderated StatisticsThis package facilitates the discovery of biomarkers from biological sequencing data (e.g., microarrays, RNA-seq) based on the associations of potential biomarkers with exposure and outcome variables by implementing an estimation procedure that combines a generalization of the moderated t-statistic with asymptotically linear statistical parameters estimated via targeted minimum loss-based estimation (TMLE).link - Attachment (Bioconductor): biotmle (development version) > This package facilitates the discovery of biomarkers from biological sequencing data (e.g., microarrays, RNA-seq) based on the associations of potential biomarkers with exposure and outcome variables by implementing an estimation procedure that combines a generalization of the moderated t-statistic with asymptotically linear statistical parameters estimated via targeted minimum loss-based estimation (TMLE).

New Packages: Bioconductor (21:06:28): > http://bioconductor.org/packages/BLMA/ BLMA BLMA: A package for bi-level meta-analysisSuit of tools for bi-level meta-analysis. The package can be used in a wide range of applications, including general hypothesis testings, differential expression analysis, functional analysis, and pathway analysis.link - Attachment (Bioconductor): BLMA (development version) > Suit of tools for bi-level meta-analysis. The package can be used in a wide range of applications, including general hypothesis testings, differential expression analysis, functional analysis, and pathway analysis.

New Packages: Bioconductor (21:06:28): > http://bioconductor.org/packages/metavizr/ metavizr R Interface to the metaviz web app for interactive metagenomics data analysis and visualizationThis package provides Websocket communication to the metaviz web app (http://metaviz.cbcb.umd.edu) for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported (e.g., MRexperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as… - Attachment (metaviz.cbcb.umd.edu): Metaviz > Epiviz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

New Packages: Bioconductor (21:06:28): > http://bioconductor.org/packages/cellbaseR/ cellbaseR Querying annotation data from the high performance Cellbase web servicesThis R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.link - Attachment (Bioconductor): cellbaseR (development version) > This R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.

New Packages: Bioconductor (21:06:28): > http://bioconductor.org/packages/PPInfer/ PPInfer Inferring functionally related proteins using protein interaction networksInteractions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn urshered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at…

New Packages: Bioconductor (21:06:28): > http://bioconductor.org/packages/ideal/ ideal Interactive Differential Expression AnaLysisThis package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package.link - Attachment (Bioconductor): ideal (development version) > This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package.

New Packages: Bioconductor (21:06:28): > http://bioconductor.org/packages/heatmaps/ heatmaps Flexible Heatmaps for Functional Genomics and Sequence FeaturesThis package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.link - Attachment (Bioconductor): heatmaps (development version) > This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.

2017-04-26

New Packages: Bioconductor (11:21:21): > http://bioconductor.org/packages/psichomics/ psichomics Graphical Interface for Alternative Splicing Quantification, Analysis and VisualisationInteractive R package with a Shiny-based graphical interface for the quantification, analysis and visualisation of alternative splicing data from The Cancer Genome Atlas (TCGA) or the Genotype-Tissue Expression (GTEx) project. This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA and GTEx samples. > > <a…

New Packages: Bioconductor (11:21:21): > http://bioconductor.org/packages/coseq/ coseq Co-Expression Analysis of Sequencing DataCo-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.link - Attachment (Bioconductor): coseq > Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.

2017-04-27

New Packages: Bioconductor (06:11:27): > http://bioconductor.org/packages/cellscape/ cellscape Explores single cell copy number profiles in the context of a single cell treeCellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of…

New Packages: Bioconductor (06:11:27): > http://bioconductor.org/packages/pathprint/ pathprint Pathway fingerprinting for analysis of gene expression arraysAlgorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.link - Attachment (Bioconductor): pathprint > Algorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.

New Packages: Bioconductor (15:51:22): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results. > > <a…

New Packages: Bioconductor (15:51:22): > http://bioconductor.org/packages/chimeraviz/ chimeraviz Visualization tools for gene fusionschimeraviz manages data from fusion gene finders and provides useful visualization tools.link - Attachment (Bioconductor): chimeraviz > chimeraviz manages data from fusion gene finders and provides useful visualization tools.

2017-04-28

New Packages: Bioconductor (20:51:50): > http://bioconductor.org/packages/gcapc/ gcapc GC Aware Peak CallerPeak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.link - Attachment (Bioconductor): gcapc > Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.

New Packages: Bioconductor (20:51:51): > http://bioconductor.org/packages/cellbaseR/ cellbaseR Querying annotation data from the high performance Cellbase web servicesThis R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.link - Attachment (Bioconductor): cellbaseR > This R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.

2017-04-29

New Packages: Bioconductor (11:01:23): > http://bioconductor.org/packages/gcapc/ gcapc GC Aware Peak CallerPeak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.link - Attachment (Bioconductor): gcapc > Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.

New Packages: Bioconductor (11:01:23): > http://bioconductor.org/packages/treeio/ treeio Base Classes and Functions for Phylogenetic Tree Input and OutputBase classes and functions for parsing and exporting phylogenetic trees.link - Attachment (Bioconductor): treeio > Base classes and functions for parsing and exporting phylogenetic trees.

New Packages: Bioconductor (21:02:03): > http://bioconductor.org/packages/gcapc/ gcapc GC Aware Peak CallerPeak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.link - Attachment (Bioconductor): gcapc > Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using weighted GC strategy, then applied into peak significance estimation.

2017-04-30

New Packages: Bioconductor (06:02:08): > http://bioconductor.org/packages/chimeraviz/ chimeraviz Visualization tools for gene fusionschimeraviz manages data from fusion gene finders and provides useful visualization tools.link - Attachment (Bioconductor): chimeraviz > chimeraviz manages data from fusion gene finders and provides useful visualization tools.

New Packages: Bioconductor (21:02:06): > http://bioconductor.org/packages/chimeraviz/ chimeraviz Visualization tools for gene fusionschimeraviz manages data from fusion gene finders and provides useful visualization tools.link - Attachment (Bioconductor): chimeraviz > chimeraviz manages data from fusion gene finders and provides useful visualization tools.

2017-05-01

New Packages: Bioconductor (05:51:51): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results. > > <a…

New Packages: Bioconductor (05:51:51): > http://bioconductor.org/packages/semisup/ semisup Detecting SNPs with interactive effects on a quantitative traitThis R packages moves away from testing interaction terms, and move towards testing whether an individual SNP is involved in any interaction. This reduces the multiple testing burden to one test per SNP, and allows for interactions with unobserved factors. Analysing one SNP at a time, it splits the individuals into two groups, based on the number of minor alleles. If the quantitative trait differs in mean between the two groups, the SNP has a main effect. If the quantitative trait differs in…

2017-05-02

New Packages: Bioconductor (16:01:58): > http://bioconductor.org/packages/RTNduals/ RTNduals Analysis of co-regulatory network motifs and inference of ‘dual regulons’RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer ‘dual regulons’, a new concept that tests whether regulon pairs agree on the predicted downstream effects.link - Attachment (Bioconductor): RTNduals > RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer ‘dual regulons’, a new concept that tests whether regulon pairs agree on the predicted downstream effects.

New Packages: Bioconductor (20:56:45): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results. > > <a…

New Packages: Bioconductor (20:56:45): > http://bioconductor.org/packages/IWTomics/ IWTomics Interval-Wise Testing for Omics DataImplementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in “Omics” data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.link - Attachment (Bioconductor): IWTomics > Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in

2017-05-03

New Packages: Bioconductor (06:01:23): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (15:56:45): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (15:56:45): > http://bioconductor.org/packages/chimeraviz/ chimeraviz Visualization tools for gene fusionschimeraviz manages data from fusion gene finders and provides useful visualization tools.link - Attachment (Bioconductor): chimeraviz > chimeraviz manages data from fusion gene finders and provides useful visualization tools.

New Packages: Bioconductor (20:51:58): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

2017-05-04

New Packages: Bioconductor (20:51:46): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

2017-05-05

New Packages: Bioconductor (00:51:47): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (10:51:44): > http://bioconductor.org/packages/anamiR/ anamiR An integrated analysis package of miRNA and mRNA expression dataThis package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.link - Attachment (Bioconductor): anamiR > This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.

New Packages: Bioconductor (15:51:50): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results. > > <a…

New Packages: Bioconductor (15:51:51): > http://bioconductor.org/packages/RTNduals/ RTNduals Analysis of co-regulatory network motifs and inference of ‘dual regulons’RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer ‘dual regulons’, a new concept that tests whether regulon pairs agree on the predicted downstream effects.link - Attachment (Bioconductor): RTNduals > RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer ‘dual regulons’, a new concept that tests whether regulon pairs agree on the predicted downstream effects.

New Packages: Bioconductor (15:51:51): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

2017-05-06

New Packages: Bioconductor (05:46:56): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

2017-05-08

New Packages: Bioconductor (15:46:55): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (15:46:55): > http://bioconductor.org/packages/TReNA/ TReNA Fit transcriptional regulatory networks using gene expression, priors, machine learningMethods for reconstructing transcriptional regulatory networks, especially in species for which genome-wide TF binding site information is available.link - Attachment (Bioconductor): TReNA (development version) > Methods for reconstructing transcriptional regulatory networks, especially in species for which genome-wide TF binding site information is available.

New Packages: Bioconductor (15:46:55): > http://bioconductor.org/packages/GA4GHshiny/ GA4GHshiny Shiny application for interacting with GA4GH-based data serversGA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network.link - Attachment (Bioconductor): GA4GHshiny (development version) > GA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network.

New Packages: Bioconductor (15:46:55): > http://bioconductor.org/packages/DASC/ DASC Detecting hidden batch factors through data adaptive adjustment for biological effectsThe package is used for identifying batches in high-dimensional dataset.link - Attachment (Bioconductor): DASC (development version) > The package is used for identifying batches in high-dimensional dataset.

2017-05-11

New Packages: Bioconductor (11:01:29): > http://bioconductor.org/packages/epiNEM/ epiNEM epiNEMepiNEM is an extension of the original Nested Effects Models (NEM). EpiNEM is able to take into account double knockouts and infer more complex network signalling pathways.link - Attachment (Bioconductor): epiNEM > epiNEM is an extension of the original Nested Effects Models (NEM). EpiNEM is able to take into account double knockouts and infer more complex network signalling pathways.

New Packages: Bioconductor (20:51:47): > http://bioconductor.org/packages/ATACseqQC/ ATACseqQC ATAC-seq Quality ControlATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To…

2017-05-12

New Packages: Bioconductor (10:52:00): > http://bioconductor.org/packages/StarBioTrek/ StarBioTrek StarBioTrek <<<<<<< .mineThis tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.link - Attachment (Bioconductor): StarBioTrek > This tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.

New Packages: Bioconductor (15:56:46): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

2017-05-13

New Packages: Bioconductor (06:01:49): > http://bioconductor.org/packages/CATALYST/ CATALYST Cytometry dATa anALYSis ToolsMass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to…

2017-05-15

New Packages: Bioconductor (10:56:44): > http://bioconductor.org/packages/BioCor/ BioCor Functional similaritiesCalculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships…link - Attachment (Bioconductor): BioCor > Calculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships…

2017-05-16

New Packages: Bioconductor (10:51:49): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results. > > <a…

New Packages: Bioconductor (15:56:45): > http://bioconductor.org/packages/AnnotationFilter/ AnnotationFilter Facilities for Filtering Bioconductor Annotation ResourcesThis package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.link - Attachment (Bioconductor): AnnotationFilter > This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.

2017-05-18

New Packages: Bioconductor (05:52:20): > http://bioconductor.org/packages/MCbiclust/ MCbiclust Massive correlating biclusters for gene expression data and associated methodsCustom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.link - Attachment (Bioconductor): MCbiclust > Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

New Packages: Bioconductor (05:52:20): > http://bioconductor.org/packages/pathprint/ pathprint Pathway fingerprinting for analysis of gene expression arraysAlgorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.link - Attachment (Bioconductor): pathprint > Algorithms to convert a gene expression array provided as an expression table or a GEO reference to a ‘pathway fingerprint’, a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.

New Packages: Bioconductor (11:01:35): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

New Packages: Bioconductor (20:57:31): > http://bioconductor.org/packages/metavizr/ metavizr R Interface to the metaviz web app for interactive metagenomics data analysis and visualizationThis package provides Websocket communication to the metaviz web app (http://metaviz.cbcb.umd.edu) for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported (e.g., MRexperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as… - Attachment (metaviz.cbcb.umd.edu): Metaviz > Epiviz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

2017-05-19

New Packages: Bioconductor (05:52:03): > http://bioconductor.org/packages/BioCor/ BioCor Functional similaritiesCalculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships…link - Attachment (Bioconductor): BioCor > Calculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships…

2017-05-20

New Packages: Bioconductor (00:56:35): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (20:55:44): > http://bioconductor.org/packages/gcapc/ gcapc GC Aware Peak CallerPeak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.link - Attachment (Bioconductor): gcapc > Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.

2017-05-24

New Packages: Bioconductor (16:01:30): > http://bioconductor.org/packages/cydar/ cydar Using Mass Cytometry for Differential Abundance AnalysesIdentifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.link - Attachment (Bioconductor): cydar > Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.

New Packages: Bioconductor (16:01:30): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

New Packages: Bioconductor (16:01:30): > http://bioconductor.org/packages/ATACseqQC/ ATACseqQC ATAC-seq Quality ControlATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To…

New Packages: Bioconductor (21:01:30): > http://bioconductor.org/packages/RaggedExperiment/ RaggedExperiment Representation of Sparse Experiments and Assays Across SamplesThis package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns.link - Attachment (Bioconductor): RaggedExperiment > This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns.

2017-05-25

New Packages: Bioconductor (01:06:32): > http://bioconductor.org/packages/PPInfer/ PPInfer Inferring functionally related proteins using protein interaction networksInteractions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at…

New Packages: Bioconductor (10:51:34): > http://bioconductor.org/packages/chimeraviz/ chimeraviz Visualization tools for gene fusionschimeraviz manages data from fusion gene finders and provides useful visualization tools.link - Attachment (Bioconductor): chimeraviz > chimeraviz manages data from fusion gene finders and provides useful visualization tools.

New Packages: Bioconductor (20:53:55): > http://bioconductor.org/packages/PPInfer/ PPInfer Inferring functionally related proteins using protein interaction networksInteractions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at…

2017-05-28

New Packages: Bioconductor (15:59:00): > http://bioconductor.org/packages/ATACseqQC/ ATACseqQC ATAC-seq Quality ControlATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To…

2017-05-29

New Packages: Bioconductor (01:04:17): > http://bioconductor.org/packages/rqt/ rqt rqt: utilities for gene-level meta-analysisDespite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: “Gene-set association tests for next-generation sequencing data” by Lee et al (2016), Bioinformatics, 32(17), i611-i619,http://bioconductor.org/packages/rqt/ - Attachment (Bioconductor): rqt > Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see:

2017-05-30

New Packages: Bioconductor (10:53:47): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results. > > <a…

New Packages: Bioconductor (10:53:47): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (10:53:47): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

New Packages: Bioconductor (15:59:04): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results. > > <a…

2017-05-31

New Packages: Bioconductor (16:58:50): > http://bioconductor.org/packages/IWTomics/ IWTomics Interval-Wise Testing for Omics DataImplementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in “Omics” data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.link - Attachment (Bioconductor): IWTomics > Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in

New Packages: Bioconductor (16:58:50): > http://bioconductor.org/packages/goSTAG/ goSTAG A tool to use GO Subtrees to Tag and Annotate Genes within a setGene lists derived from the results of genomic analyses are rich in biological information. For instance, differentially expressed genes (DEGs) from a microarray or RNA-Seq analysis are related functionally in terms of their response to a treatment or condition. Gene lists can vary in size, up to several thousand genes, depending on the robustness of the perturbations or how widely different the conditions are biologically. Having a way to associate biological relatedness between hundreds and…

New Packages: Bioconductor (20:49:13): > http://bioconductor.org/packages/gcapc/ gcapc GC Aware Peak CallerPeak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.link - Attachment (Bioconductor): gcapc > Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.

2017-06-01

New Packages: Bioconductor (00:59:12): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

Davide Risso (12:43:20): > @Davide Risso has joined the channel

2017-06-02

New Packages: Bioconductor (05:54:10): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results. > > <a…

New Packages: Bioconductor (05:54:10): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (10:59:10): > http://bioconductor.org/packages/goSTAG/ goSTAG A tool to use GO Subtrees to Tag and Annotate Genes within a setGene lists derived from the results of genomic analyses are rich in biological information. For instance, differentially expressed genes (DEGs) from a microarray or RNA-Seq analysis are related functionally in terms of their response to a treatment or condition. Gene lists can vary in size, up to several thousand genes, depending on the robustness of the perturbations or how widely different the conditions are biologically. Having a way to associate biological relatedness between hundreds and…

New Packages: Bioconductor (16:19:20): > http://bioconductor.org/packages/chimeraviz/ chimeraviz Visualization tools for gene fusionschimeraviz manages data from fusion gene finders and provides useful visualization tools.link - Attachment (Bioconductor): chimeraviz > chimeraviz manages data from fusion gene finders and provides useful visualization tools.

New Packages: Bioconductor (20:48:59): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

2017-06-05

New Packages: Bioconductor (00:53:45): > http://bioconductor.org/packages/gcapc/ gcapc GC Aware Peak CallerPeak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.link - Attachment (Bioconductor): gcapc > Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.

New Packages: Bioconductor (15:58:49): > http://bioconductor.org/packages/goSTAG/ goSTAG A tool to use GO Subtrees to Tag and Annotate Genes within a setGene lists derived from the results of genomic analyses are rich in biological information. For instance, differentially expressed genes (DEGs) from a microarray or RNA-Seq analysis are related functionally in terms of their response to a treatment or condition. Gene lists can vary in size, up to several thousand genes, depending on the robustness of the perturbations or how widely different the conditions are biologically. Having a way to associate biological relatedness between hundreds and…

New Packages: Bioconductor (15:58:49): > http://bioconductor.org/packages/GA4GHshiny/ GA4GHshiny Shiny application for interacting with GA4GH-based data serversGA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network.link - Attachment (Bioconductor): GA4GHshiny (development version) > GA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network.

2017-06-06

New Packages: Bioconductor (10:54:15): > http://bioconductor.org/packages/proFIA/ proFIA Preprocessing of FIA-HRMS dataFlow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and…

New Packages: Bioconductor (20:59:12): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

2017-06-07

New Packages: Bioconductor (00:54:11): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (06:04:00): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

2017-06-08

New Packages: Bioconductor (10:48:53): > http://bioconductor.org/packages/Organism.dplyr/ Organism.dplyr dplyr-based Access to Bioconductor Annotation ResourcesThis package provides an alternative interface to Bioconductor ‘annotation’ resources, in particular the gene identifier mapping functionality of the ‘org’ packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ‘TxDb’ packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).link - Attachment (Bioconductor): Organism.dplyr > This package provides an alternative interface to Bioconductor ‘annotation’ resources, in particular the gene identifier mapping functionality of the ‘org’ packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ‘TxDb’ packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

New Packages: Bioconductor (15:54:02): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results. > > <a…

New Packages: Bioconductor (15:54:02): > http://bioconductor.org/packages/IWTomics/ IWTomics Interval-Wise Testing for Omics DataImplementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in “Omics” data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.link - Attachment (Bioconductor): IWTomics > Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in

New Packages: Bioconductor (15:54:02): > http://bioconductor.org/packages/gcapc/ gcapc GC Aware Peak CallerPeak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.link - Attachment (Bioconductor): gcapc > Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.

New Packages: Bioconductor (15:54:02): > http://bioconductor.org/packages/basecallQC/ basecallQC Working with Illumina Basecalling and Demultiplexing input and output filesThe basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions = 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages…

New Packages: Bioconductor (20:54:03): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

2017-06-09

New Packages: Bioconductor (00:53:48): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (05:59:17): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (05:59:17): > http://bioconductor.org/packages/karyoploteR/ karyoploteR Plot customizable linear genomes displaying arbitrary datakaryoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.link - Attachment (Bioconductor): karyoploteR > karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

New Packages: Bioconductor (05:59:17): > http://bioconductor.org/packages/CATALYST/ CATALYST Cytometry dATa anALYSis ToolsMass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to…

New Packages: Bioconductor (15:58:51): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (15:58:51): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

New Packages: Bioconductor (20:49:13): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

2017-06-10

New Packages: Bioconductor (20:59:28): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

2017-06-11

New Packages: Bioconductor (05:49:22): > http://bioconductor.org/packages/MWASTools/ MWASTools MWASTools: an integrated pipeline to perform metabolome-wide association studiesMWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results. > > <a…

2017-06-13

New Packages: Bioconductor (10:59:11): > http://bioconductor.org/packages/AnnotationFilter/ AnnotationFilter Facilities for Filtering Bioconductor Annotation ResourcesThis package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.link - Attachment (Bioconductor): AnnotationFilter > This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.

New Packages: Bioconductor (16:04:00): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (16:04:00): > http://bioconductor.org/packages/Organism.dplyr/ Organism.dplyr dplyr-based Access to Bioconductor Annotation ResourcesThis package provides an alternative interface to Bioconductor ‘annotation’ resources, in particular the gene identifier mapping functionality of the ‘org’ packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ‘TxDb’ packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).link - Attachment (Bioconductor): Organism.dplyr > This package provides an alternative interface to Bioconductor ‘annotation’ resources, in particular the gene identifier mapping functionality of the ‘org’ packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ‘TxDb’ packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

New Packages: Bioconductor (16:04:00): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

New Packages: Bioconductor (20:49:11): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (20:49:12): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

2017-06-14

New Packages: Bioconductor (00:48:58): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (05:48:58): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (15:53:56): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (15:53:57): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

New Packages: Bioconductor (20:53:53): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (20:53:53): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

2017-06-15

New Packages: Bioconductor (00:54:00): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (05:49:10): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (05:49:10): > http://bioconductor.org/packages/CATALYST/ CATALYST Cytometry dATa anALYSis ToolsMass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to…

New Packages: Bioconductor (16:04:14): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

New Packages: Bioconductor (16:04:14): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

New Packages: Bioconductor (21:03:53): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

2017-06-16

New Packages: Bioconductor (15:48:59): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

New Packages: Bioconductor (15:48:59): > http://bioconductor.org/packages/IntEREst/ IntEREst Intron-Exon Retention EstimatorThis package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).link - Attachment (Bioconductor): IntEREst > This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).

2017-06-17

New Packages: Bioconductor (05:59:15): > http://bioconductor.org/packages/PPInfer/ PPInfer Inferring functionally related proteins using protein interaction networksInteractions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at…

New Packages: Bioconductor (15:58:49): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

2017-06-18

New Packages: Bioconductor (00:58:56): > http://bioconductor.org/packages/PPInfer/ PPInfer Inferring functionally related proteins using protein interaction networksInteractions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at…

New Packages: Bioconductor (06:09:11): > http://bioconductor.org/packages/PPInfer/ PPInfer Inferring functionally related proteins using protein interaction networksInteractions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at…

2017-06-19

New Packages: Bioconductor (11:23:47): > http://bioconductor.org/packages/Organism.dplyr/ Organism.dplyr dplyr-based Access to Bioconductor Annotation ResourcesThis package provides an alternative interface to Bioconductor ‘annotation’ resources, in particular the gene identifier mapping functionality of the ‘org’ packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ‘TxDb’ packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).link - Attachment (Bioconductor): Organism.dplyr > This package provides an alternative interface to Bioconductor ‘annotation’ resources, in particular the gene identifier mapping functionality of the ‘org’ packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ‘TxDb’ packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

New Packages: Bioconductor (11:23:47): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

New Packages: Bioconductor (15:48:57): > http://bioconductor.org/packages/miRBaseConverter/ miRBaseConverter A converter for miRNA Name, Accession ID and Sequence in different miRBase VersionsmiRBaseConverter is a comprehensive tool for the miRNA information retrieval and conversion in miRBase versions. As an R/Bioconductor package, it is mianly desighed for converting and retrieving the definition of miRNAs ( Names, Accession IDs, Sequences, Families and others) in miRBase different versions. It can process a huge number of miRNAs in short time without any other depends.link - Attachment (Bioconductor): miRBaseConverter (development version) > miRBaseConverter is designed for miRBase conversion between miRNA Names, Accession ID and Sequence in different updated versions. The package involves a small build-in database without any other depends. It can process a huge number of miRNAs in very short time.

2017-06-20

New Packages: Bioconductor (05:59:11): > http://bioconductor.org/packages/CATALYST/ CATALYST Cytometry dATa anALYSis ToolsMass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to…

New Packages: Bioconductor (16:23:59): > http://bioconductor.org/packages/GA4GHclient/ GA4GHclient A Bioconductor package for accessing GA4GH API data serversGA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.link - Attachment (Bioconductor): GA4GHclient > GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.

New Packages: Bioconductor (16:23:59): > http://bioconductor.org/packages/GA4GHshiny/ GA4GHshiny Shiny application for interacting with GA4GH-based data serversGA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network.link - Attachment (Bioconductor): GA4GHshiny (development version) > GA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network.

2017-06-21

New Packages: Bioconductor (20:14:05): > http://bioconductor.org/packages/karyoploteR/ karyoploteR Plot customizable linear genomes displaying arbitrary datakaryoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.link - Attachment (Bioconductor): karyoploteR > karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

New Packages: Bioconductor (20:54:00): > http://bioconductor.org/packages/DelayedArray/ DelayedArray Delayed operations on array-like objectsWrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames….

2017-06-22

New Packages: Bioconductor (20:59:06): > http://bioconductor.org/packages/Organism.dplyr/ Organism.dplyr dplyr-based Access to Bioconductor Annotation ResourcesThis package provides an alternative interface to Bioconductor ‘annotation’ resources, in particular the gene identifier mapping functionality of the ‘org’ packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ‘TxDb’ packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).link - Attachment (Bioconductor): Organism.dplyr > This package provides an alternative interface to Bioconductor ‘annotation’ resources, in particular the gene identifier mapping functionality of the ‘org’ packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ‘TxDb’ packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

2017-06-23

New Packages: Bioconductor (10:53:49): > http://bioconductor.org/packages/MIGSA/ MIGSA Massive and Integrative Gene Set AnalysisMassive and Integrative Gene Set Analysis. The MIGSA package allows to perform a massive and integrative gene set analysis over several expression and gene sets simultaneously. It provides a common gene expression analytic framework that grants a comprehensive and coherent analysis. Only a minimal user parameter setting is required to perform both singular and gene set enrichment analyses in an integrative manner by means of the best available methods, i.e. dEnricher and…

2017-06-24

New Packages: Bioconductor (15:49:10): > http://bioconductor.org/packages/gcapc/ gcapc GC Aware Peak CallerPeak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.link - Attachment (Bioconductor): gcapc > Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.

2017-06-26

New Packages: Bioconductor (21:04:14): > http://bioconductor.org/packages/AnnotationFilter/ AnnotationFilter Facilities for Filtering Bioconductor Annotation ResourcesThis package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.link - Attachment (Bioconductor): AnnotationFilter > This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.

2017-06-27

New Packages: Bioconductor (16:25:28): > http://bioconductor.org/packages/coseq/ coseq Co-Expression Analysis of Sequencing DataCo-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.link - Attachment (Bioconductor): coseq > Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.

New Packages: Bioconductor (16:25:28): > http://bioconductor.org/packages/REMP/ REMP Repetitive Element Methylation PredictionMachine learing-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE. > > <a…

New Packages: Bioconductor (16:25:28): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

2017-06-28

New Packages: Bioconductor (10:58:47): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

2017-06-29

New Packages: Bioconductor (20:49:10): > http://bioconductor.org/packages/rqt/ rqt rqt: utilities for gene-level meta-analysisDespite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: “Gene-set association tests for next-generation sequencing data” by Lee et al (2016), Bioinformatics, 32(17), i611-i619,http://bioconductor.org/packages/rqt/ - Attachment (Bioconductor): rqt > Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see:

2017-06-30

New Packages: Bioconductor (15:58:58): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

Davide Risso (18:57:23): > @Davide Risso has left the channel

New Packages: Bioconductor (20:53:47): > http://bioconductor.org/packages/scone/ scone Single Cell Overview of Normalized Expression dataSCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.link - Attachment (Bioconductor): scone > SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.

2017-07-03

New Packages: Bioconductor (05:59:09): > http://bioconductor.org/packages/CATALYST/ CATALYST Cytometry dATa anALYSis ToolsMass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to…

New Packages: Bioconductor (15:48:55): > http://bioconductor.org/packages/scone/ scone Single Cell Overview of Normalized Expression dataSCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.link - Attachment (Bioconductor): scone > SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.

New Packages: Bioconductor (20:48:47): > http://bioconductor.org/packages/zinbwave/ zinbwave Zero-Inflated Negative Binomial Model for RNA-Seq DataImplements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.link - Attachment (Bioconductor): zinbwave (development version) > Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.

2017-07-04

New Packages: Bioconductor (15:48:42): > http://bioconductor.org/packages/karyoploteR/ karyoploteR Plot customizable linear genomes displaying arbitrary datakaryoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.link - Attachment (Bioconductor): karyoploteR > karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

2017-07-05

New Packages: Bioconductor (11:03:58): > http://bioconductor.org/packages/zinbwave/ zinbwave Zero-Inflated Negative Binomial Model for RNA-Seq DataImplements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.link - Attachment (Bioconductor): zinbwave (development version) > Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.

2017-07-07

New Packages: Bioconductor (00:53:47): > http://bioconductor.org/packages/splatter/ splatter Simple Simulation of Single-cell RNA Sequencing DataSplatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.link - Attachment (Bioconductor): splatter > Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.

New Packages: Bioconductor (15:59:11): > http://bioconductor.org/packages/IntEREst/ IntEREst Intron-Exon Retention EstimatorThis package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).link - Attachment (Bioconductor): IntEREst > This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).

2017-07-08

New Packages: Bioconductor (15:53:43): > http://bioconductor.org/packages/miRBaseConverter/ miRBaseConverter A comprehensive tool for converting and retrieving miRNA information in miRBase historical versions.A comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version and Family information in miRBase historical versions. It can process a huge number of miRNAs in short time without other depends.link - Attachment (Bioconductor): miRBaseConverter (development version) > miRBaseConverter is a comprehensive tool for the miRNA information retrieval and conversion in miRBase versions. As an R/Bioconductor package, it is mianly desighed for converting and retrieving the definition of miRNAs ( Names, Accession IDs, Sequences, Families and others) in miRBase different versions. It can process a huge number of miRNAs in short time without any other depends.

New Packages: Bioconductor (20:48:56): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

2017-07-09

New Packages: Bioconductor (15:59:05): > http://bioconductor.org/packages/miRBaseConverter/ miRBaseConverter A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versionsA comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends.link - Attachment (Bioconductor): miRBaseConverter (development version) > A comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version and Family information in miRBase historical versions. It can process a huge number of miRNAs in short time without other depends.

2017-07-10

New Packages: Bioconductor (15:53:52): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

New Packages: Bioconductor (21:04:14): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

New Packages: Bioconductor (21:04:14): > http://bioconductor.org/packages/RProtoBufLib/ RProtoBufLib C++ headers and static libraries of Protocol buffersThis package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against.link - Attachment (Bioconductor): RProtoBufLib (development version) > This package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against.

New Packages: Bioconductor (21:04:14): > http://bioconductor.org/packages/Rhdf5lib/ Rhdf5lib hdf5 library as an R packageProvides C and C++ hdf5 libraries.link - Attachment (Bioconductor): Rhdf5lib (development version) > Provides C and C++ hdf5 libraries.

2017-07-11

New Packages: Bioconductor (00:59:11): > http://bioconductor.org/packages/branchpointer/ branchpointer Prediction of intronic splicing branchpointsPredicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.link - Attachment (Bioconductor): branchpointer > Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.

New Packages: Bioconductor (15:54:02): > http://bioconductor.org/packages/Rhdf5lib/ Rhdf5lib hdf5 library as an R packageProvides C and C++ hdf5 libraries.link - Attachment (Bioconductor): Rhdf5lib (development version) > Provides C and C++ hdf5 libraries.

2017-07-12

New Packages: Bioconductor (10:54:02): > http://bioconductor.org/packages/MCbiclust/ MCbiclust Massive correlating biclusters for gene expression data and associated methodsCustom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.link - Attachment (Bioconductor): MCbiclust > Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

New Packages: Bioconductor (10:54:02): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

New Packages: Bioconductor (10:54:02): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

2017-07-13

New Packages: Bioconductor (17:49:04): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

New Packages: Bioconductor (17:49:04): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

New Packages: Bioconductor (20:58:51): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

2017-07-14

New Packages: Bioconductor (00:48:44): > http://bioconductor.org/packages/branchpointer/ branchpointer Prediction of intronic splicing branchpointsPredicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.link - Attachment (Bioconductor): branchpointer > Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.

New Packages: Bioconductor (10:53:59): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

New Packages: Bioconductor (15:58:52): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

2017-07-15

New Packages: Bioconductor (15:59:07): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

New Packages: Bioconductor (15:59:07): > http://bioconductor.org/packages/SingleCellExperiment/ SingleCellExperiment S4 Classes for Single Cell DataDefines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.link - Attachment (Bioconductor): SingleCellExperiment (development version) > Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.

New Packages: Bioconductor (15:59:07): > http://bioconductor.org/packages/consensusOV/ consensusOV Gene expression-based subtype classification for high-grade serous ovarian cancerThis package implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer as described by Helland et al. (PLoS One, 2011), Bentink et al. (PLoS One, 2012), Verhaak et al. (J Clin Invest, 2013), and Konecny et al. (J Natl Cancer Inst, 2014). In addition, the package implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of…

2017-07-16

New Packages: Bioconductor (00:49:15): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

New Packages: Bioconductor (05:58:58): > http://bioconductor.org/packages/splatter/ splatter Simple Simulation of Single-cell RNA Sequencing DataSplatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.link - Attachment (Bioconductor): splatter > Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.

New Packages: Bioconductor (10:49:13): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

New Packages: Bioconductor (20:59:11): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

2017-07-17

New Packages: Bioconductor (05:54:11): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

New Packages: Bioconductor (05:54:11): > http://bioconductor.org/packages/Rhdf5lib/ Rhdf5lib hdf5 library as an R packageProvides C and C++ hdf5 libraries.link - Attachment (Bioconductor): Rhdf5lib (development version) > Provides C and C++ hdf5 libraries.

New Packages: Bioconductor (10:49:13): > http://bioconductor.org/packages/MCbiclust/ MCbiclust Massive correlating biclusters for gene expression data and associated methodsCustom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.link - Attachment (Bioconductor): MCbiclust > Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

New Packages: Bioconductor (10:49:13): > http://bioconductor.org/packages/twoddpcr/ twoddpcr Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting moleculesThe twoddpcr package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad’s QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data. Previous work includes ‘definetherain’ (Jones et al., 2014) and ‘ddpcRquant’…

New Packages: Bioconductor (10:49:14): > http://bioconductor.org/packages/Rhdf5lib/ Rhdf5lib hdf5 library as an R packageProvides C and C++ hdf5 libraries.link - Attachment (Bioconductor): Rhdf5lib (development version) > Provides C and C++ hdf5 libraries.

New Packages: Bioconductor (15:59:11): > http://bioconductor.org/packages/Rhdf5lib/ Rhdf5lib hdf5 library as an R packageProvides C and C++ hdf5 libraries.link - Attachment (Bioconductor): Rhdf5lib (development version) > Provides C and C++ hdf5 libraries.

New Packages: Bioconductor (20:59:02): > http://bioconductor.org/packages/Rhdf5lib/ Rhdf5lib hdf5 library as an R packageProvides C and C++ hdf5 libraries.link - Attachment (Bioconductor): Rhdf5lib (development version) > Provides C and C++ hdf5 libraries.

2017-07-18

New Packages: Bioconductor (05:54:13): > http://bioconductor.org/packages/CATALYST/ CATALYST Cytometry dATa anALYSis ToolsMass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to…

New Packages: Bioconductor (10:59:11): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

New Packages: Bioconductor (20:53:46): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

2017-07-19

New Packages: Bioconductor (06:04:03): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

New Packages: Bioconductor (10:54:14): > http://bioconductor.org/packages/metavizr/ metavizr R Interface to the metaviz web app for interactive metagenomics data analysis and visualizationThis package provides Websocket communication to the metaviz web app (http://metaviz.cbcb.umd.edu) for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported (e.g., MRexperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as… - Attachment (metaviz.cbcb.umd.edu): Metaviz > Metaviz is a scientific information visualization tool for metagenomic data, used to aid in the exploration of the hierarchical taxonomy and abundance matrix.

2017-07-20

New Packages: Bioconductor (00:54:11): > http://bioconductor.org/packages/treeio/ treeio Base Classes and Functions for Phylogenetic Tree Input and OutputBase classes and functions for parsing and exporting phylogenetic trees.link - Attachment (Bioconductor): treeio > Base classes and functions for parsing and exporting phylogenetic trees.

New Packages: Bioconductor (00:54:11): > http://bioconductor.org/packages/splatter/ splatter Simple Simulation of Single-cell RNA Sequencing DataSplatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.link - Attachment (Bioconductor): splatter > Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.

New Packages: Bioconductor (00:54:11): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

New Packages: Bioconductor (10:54:12): > http://bioconductor.org/packages/beachmat/ beachmat Compiling Bioconductor to Handle Each Matrix TypeProvides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.link - Attachment (Bioconductor): beachmat (development version) > Provides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.

New Packages: Bioconductor (15:53:52): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

New Packages: Bioconductor (20:54:13): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

New Packages: Bioconductor (20:54:13): > http://bioconductor.org/packages/RProtoBufLib/ RProtoBufLib C++ headers and static libraries of Protocol buffersThis package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against.link - Attachment (Bioconductor): RProtoBufLib (development version) > This package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against.

2017-07-21

New Packages: Bioconductor (06:04:11): > http://bioconductor.org/packages/GenomicScores/ GenomicScores Infrastructure to work with genomewide position-specific scoresProvide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.link - Attachment (Bioconductor): GenomicScores > Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

New Packages: Bioconductor (15:59:16): > http://bioconductor.org/packages/beachmat/ beachmat Compiling Bioconductor to Handle Each Matrix TypeProvides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.link - Attachment (Bioconductor): beachmat (development version) > Provides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.

New Packages: Bioconductor (20:59:01): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

2017-07-23

New Packages: Bioconductor (00:58:49): > http://bioconductor.org/packages/ATACseqQC/ ATACseqQC ATAC-seq Quality ControlATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To…

New Packages: Bioconductor (05:48:58): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

New Packages: Bioconductor (11:03:51): > http://bioconductor.org/packages/beachmat/ beachmat Compiling Bioconductor to Handle Each Matrix TypeProvides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.link - Attachment (Bioconductor): beachmat (development version) > Provides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.

2017-07-24

New Packages: Bioconductor (01:03:59): > http://bioconductor.org/packages/mapscape/ mapscape mapscapeMapScape integrates clonal prevalence, clonal hierarchy, anatomic and mutational information to provide interactive visualization of spatial clonal evolution. There are four inputs to MapScape: (i) the clonal phylogeny, (ii) clonal prevalences, (iii) an image reference, which may be a medical image or drawing and (iv) pixel locations for each sample on the referenced image. Optionally, MapScape can accept a data table of mutations for each clone and their variant allele frequencies in each…

New Packages: Bioconductor (06:03:50): > http://bioconductor.org/packages/CATALYST/ CATALYST Cytometry dATa anALYSis ToolsMass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to…

New Packages: Bioconductor (20:54:14): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

2017-07-25

New Packages: Bioconductor (00:53:51): > http://bioconductor.org/packages/NADfinder/ NADfinder Call wide peaks for sequencing dataNucleolus is an important structure inside the nucleus in eukaryotic cells. It is the site for transcribing rDNA into rRNA and for assembling ribosomes, aka ribosome biogenesis. In addition, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non-rDNA genomic loci. Deep sequencing analyses of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci, termed nucleolar- associated domains (NADs) form frequent three- dimensional…

New Packages: Bioconductor (20:58:52): > http://bioconductor.org/packages/RProtoBufLib/ RProtoBufLib C++ headers and static libraries of Protocol buffersThis package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against.link - Attachment (Bioconductor): RProtoBufLib (development version) > This package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against.

2017-07-26

Ju Yeong Kim (14:37:20): > @Ju Yeong Kim has joined the channel

2017-07-28

Leonardo Collado Torres (09:22:46): > @Leonardo Collado Torres has joined the channel

New Packages: Bioconductor (15:53:56): > http://bioconductor.org/packages/twoddpcr/ twoddpcr Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting moleculesThe twoddpcr package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad’s QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data. Previous work includes ‘definetherain’ (Jones et al., 2014) and ‘ddpcRquant’…

New Packages: Bioconductor (15:53:56): > http://bioconductor.org/packages/RProtoBufLib/ RProtoBufLib C++ headers and static libraries of Protocol buffersThis package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against.link - Attachment (Bioconductor): RProtoBufLib (development version) > This package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against.

2017-07-30

New Packages: Bioconductor (15:48:49): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

2017-07-31

New Packages: Bioconductor (10:59:18): > http://bioconductor.org/packages/twoddpcr/ twoddpcr Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting moleculesThe twoddpcr package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad’s QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data. Previous work includes ‘definetherain’ (Jones et al., 2014) and ‘ddpcRquant’…

New Packages: Bioconductor (10:59:19): > http://bioconductor.org/packages/CATALYST/ CATALYST Cytometry dATa anALYSis ToolsMass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to…

New Packages: Bioconductor (16:39:13): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

New Packages: Bioconductor (16:39:13): > http://bioconductor.org/packages/RaggedExperiment/ RaggedExperiment Representation of Sparse Experiments and Assays Across SamplesThis package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns.link - Attachment (Bioconductor): RaggedExperiment > This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns.

2017-08-01

New Packages: Bioconductor (00:49:14): > http://bioconductor.org/packages/PPInfer/ PPInfer Inferring functionally related proteins using protein interaction networksInteractions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at…

New Packages: Bioconductor (10:49:03): > http://bioconductor.org/packages/IntEREst/ IntEREst Intron-Exon Retention EstimatorThis package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).link - Attachment (Bioconductor): IntEREst > This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).

New Packages: Bioconductor (15:54:00): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

2017-08-03

New Packages: Bioconductor (05:59:12): > http://bioconductor.org/packages/miRBaseConverter/ miRBaseConverter A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versionsA comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends.link - Attachment (Bioconductor): miRBaseConverter (development version) > A comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends.

New Packages: Bioconductor (15:59:13): > http://bioconductor.org/packages/Organism.dplyr/ Organism.dplyr dplyr-based Access to Bioconductor Annotation ResourcesThis package provides an alternative interface to Bioconductor ‘annotation’ resources, in particular the gene identifier mapping functionality of the ‘org’ packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ‘TxDb’ packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).link - Attachment (Bioconductor): Organism.dplyr > This package provides an alternative interface to Bioconductor ‘annotation’ resources, in particular the gene identifier mapping functionality of the ‘org’ packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ‘TxDb’ packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

New Packages: Bioconductor (15:59:13): > http://bioconductor.org/packages/BiocFileCache/ BiocFileCache Manage Files Across SessionsThis package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.link - Attachment (Bioconductor): BiocFileCache > This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

New Packages: Bioconductor (20:53:54): > http://bioconductor.org/packages/beachmat/ beachmat Compiling Bioconductor to Handle Each Matrix TypeProvides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.link - Attachment (Bioconductor): beachmat (development version) > Provides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.

2017-08-04

New Packages: Bioconductor (00:53:48): > http://bioconductor.org/packages/splatter/ splatter Simple Simulation of Single-cell RNA Sequencing DataSplatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.link - Attachment (Bioconductor): splatter > Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.

New Packages: Bioconductor (20:58:52): > http://bioconductor.org/packages/TCGAbiolinksGUI/ TCGAbiolinksGUI “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data”“TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found inhttps://tcgabiolinksgui.shinyapps.io/tcgabiolinks/”link - Attachment (Bioconductor): TCGAbiolinksGUI

2017-08-05

New Packages: Bioconductor (05:59:16): > http://bioconductor.org/packages/miRBaseConverter/ miRBaseConverter A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versionsA comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends.link - Attachment (Bioconductor): miRBaseConverter (development version) > A comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends.

2017-08-08

New Packages: Bioconductor (15:49:10): > http://bioconductor.org/packages/RVS/ RVS Computes estimates of the probability of related individuals sharing a rare variantRare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test). > > <a…

New Packages: Bioconductor (15:49:10): > http://bioconductor.org/packages/CEMiTool/ CEMiTool Finds Gene Co-expression ModulesCEMiTool improves WGCNA gene co-expression module discovery by optimizing network parameter selection. This package also perfoms enrichment analysis with the discovered modules.link - Attachment (Bioconductor): CEMiTool (development version) > CEMiTool improves WGCNA gene co-expression module discovery by optimizing network parameter selection. This package also perfoms enrichment analysis with the discovered modules.

New Packages: Bioconductor (15:49:10): > http://bioconductor.org/packages/zFPKM/ zFPKM A suite of functions to facilitate zFPKM transformationsPerform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113). Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed chromosome data. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data.link - Attachment (Bioconductor): zFPKM (development version) > Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113). Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed chromosome data. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data.

New Packages: Bioconductor (20:59:14): > http://bioconductor.org/packages/RaggedExperiment/ RaggedExperiment Representation of Sparse Experiments and Assays Across SamplesThis package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns.link - Attachment (Bioconductor): RaggedExperiment > This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns.

2017-08-10

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Kasper D. Hansen (17:10:57): > I have started to useBiocManager. Today I reinstalled the package because my devel version was problematic. I loaded it and got > > > BiocManager::install(version = "devel") > Error in repos[["CRAN"]] : subscript out of bounds > > I solved it by re-runningchooseCRANmirror(). A better error message might be good

Kasper D. Hansen (19:14:54): > thanks for making the github issue@Marcel Ramos Pérez. I thought of that only afterwards

Marcel Ramos Pérez (19:36:07): > Thanks for reporting it@Kasper D. Hansen

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stefano mangiola (21:04:21): > Hello I have a question. With on-line browsing is still not clear to me how to update an existing package (tidybulk)

2020-08-30

Lluís Revilla (07:02:09): > Was this answered on this threadhttps://community-bioc.slack.com/archives/C35G93GJH/p1598749564001000or do you want additional guidance? - Attachment: Attachment > Hello, with online browsing is not really clear how to update an existing package. Could you point to a point form guide if existing? Thanks

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