ITCR-biocondcutor projects with topics: u24ca289073
A list of repositories discovered on GitHub. The table is sortable by clicking on headers and searchable via the search box.
| Repository | Owner | Description | Stars | Last Updated |
|---|---|---|---|---|
awesome-cancer-variant-resources
|
seandavi | A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants. | 318 | 2025-03-06 |
|
MultiAssayExperiment
|
waldronlab | Bioconductor package for management of multi-assay data | 72 | 2025-08-18 |
|
SpatialExperiment
|
drighelli | 71 | 2025-05-28 | |
|
BiocParallel
|
Bioconductor | Bioconductor facilities for parallel evaluation | 68 | 2025-09-10 |
|
HGNChelper
|
waldronlab | Identify and correct invalid gene symbols | 59 | 2024-11-16 |
|
curatedTCGAData
|
waldronlab | Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects | 43 | 2025-10-24 |
|
cBioPortalData
|
waldronlab | Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment | 33 | 2025-07-21 |
|
TCGAutils
|
waldronlab | Toolbox package for organizing and working with TCGA data | 28 | 2025-07-14 |
|
DelayedArray
|
Bioconductor | A unified framework for working transparently with on-disk and in-memory array-like datasets | 27 | 2025-10-24 |
|
MultiAssayWorkshop
|
waldronlab | Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment | 24 | 2025-07-02 |
|
BiocPkgTools
|
seandavi | Computable build reports, package metadata, and download stats from the Bioconductor project | 21 | 2025-10-24 |
|
enrichOmics
|
waldronlab | Functional enrichment analysis of high-throughput omics data | 20 | 2025-01-06 |
|
AnnotationHub
|
Bioconductor | Client for the Bioconductor AnnotationHub web resource | 19 | 2025-07-25 |
|
SingleCellMultiModal
|
waldronlab | Single Cell multimodal data scripts for downloading datasets | 17 | 2025-10-24 |
|
GenomicSuperSignature
|
shbrief | Interpretation of RNAseq experiments through robust, efficient comparison to public databases | 16 | 2025-10-15 |
|
PublicDataResources
|
waldronlab | Public data resources and Bioconductor: The goal of this workshop is to introduce Bioconductor packages for finding, accessing, and using large-scale public data resources including the Gene Expression Omnibus GEO, Sequence Read Archive SRA, the Genomic Data Commons GDC, and Bioconductor-hosted curated data resources for metagenomics, pharmacogenomics PharmacoDB, and The Cancer Genome Atlas. | 15 | 2025-05-12 |
|
GSEABenchmarkeR
|
waldronlab | Reproducible GSEA Benchmarking | 13 | 2025-05-08 |
|
BiocFileCache
|
Bioconductor | Manage Files Across Sessions | 13 | 2025-08-28 |
|
HDF5Array
|
Bioconductor | HDF5 datasets as array-like objects in R | 12 | 2025-08-29 |
|
curatedOvarianData
|
waldronlab | The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer | 11 | 2025-05-05 |
|
ExperimentHub
|
Bioconductor | Client to access ExperimentHub resources | 11 | 2025-10-20 |
|
SparseArray
|
Bioconductor | High-performance sparse data representation and manipulation in R | 10 | 2025-08-29 |
|
BiocOncoTK
|
vjcitn | Bioconductor components for general cancer genomics | 10 | 2023-02-05 |
|
CNVRanger
|
waldronlab | Functionality for CNV analysis | 8 | 2025-05-08 |
|
MultiAssayExperiment.TCGA
|
waldronlab | The pipeline to produce TCGA data as MultiAssayExperiment objects | 7 | 2023-05-16 |
|
S4Arrays
|
Bioconductor | Foundation of array-like containers in Bioconductor | 7 | 2025-10-24 |
|
RaggedExperiment
|
Bioconductor | Matrix-like representations of mutation and CN data | 5 | 2025-07-10 |
|
scConform
|
ccb-hms | Uncertainty quantification for cell type annotation using conformal inference | 4 | 2024-07-25 |
|
OmicsMLRepoData
|
waldronlab | Translate Bioconductor resources into AI/ML-ready format + Manual curation/harmonization of the metadata for improved usability | 3 | 2025-09-22 |
|
state-cancer-profile-scraper
|
seandavi | Bulk access and download state cancer profiles data | 3 | 2025-10-01 |
|
GenomicFiles
|
Bioconductor | Distributed computing by file or by range | 2 | 2025-07-21 |
|
YESCDS
|
vjcitn | Cancer Data Science resources for DFCI YES for CURE | 2 | 2024-10-30 |
|
OmicsMLRepoR
|
shbrief | Bioconductor package to access the harmonized metadata through ontology | 2 | 2025-09-22 |
|
refinebioc
|
seandavi | The bridge between refine.bio and Bioconductor | 2 | 2025-03-05 |
|
oncoKBData
|
waldronlab | Expose the Onco KB API via R / Bioconductor | 1 | 2025-05-09 |
|
h5mread
|
Bioconductor | A fast HDF5 reader | 1 | 2025-08-29 |
|
BiocBuildDB
|
seandavi | Longitudinal Bioc build database | 1 | 2025-09-07 |
|
bedbaser
|
waldronlab | An R client for bedbase.org | 1 | 2025-10-12 |
|
BiocHubsIngestR
|
Bioconductor | Helper package for users to upload data to temporary BiocHubsIngest endpoints | 1 | 2025-02-27 |
|
TxRegInfra2
|
vjcitn | Software for exploring transcriptional regulatory networks, currently using MongoDB documents for various genomic feature types | 1 | 2020-12-31 |
|
xenLite
|
vjcitn | Lightweight approach to managing Xenium experiments | 1 | 2024-11-27 |
|
curatedMetagenomicDataODM
|
shbrief | Genestack's Open Data Management (ODM) setup for curatedMetagenomicData curation | 1 | 2025-07-28 |
|
VisiumIO
|
waldronlab | Import spaceranger output and 10X spatial data | 1 | 2025-10-24 |
|
ITCR-bioconductor
|
waldronlab | Tracking for project 1U24CA289073-01 | 0 | 2025-08-14 |
|
RaggedExperiment_SoftNote
|
waldronlab | exploration of RaggedExperiment | 0 | 2025-01-06 |
|
hovernethelp
|
hpages | 0 | 2025-08-31 | |
|
XeniumIO
|
waldronlab | software for importing 10X Xenium data | 0 | 2025-07-03 |
|
programets
|
nih-cfde | 0 | 2025-09-22 | |
|
HGNCREST
|
waldronlab | Query the HGNC REST API with R | 0 | 2025-05-09 |
|
TENxIO
|
waldronlab | Bioconductor interface to 10X files | 0 | 2025-10-07 |