A slide deck providing a workshop overview is available here.
The goal of this workshop is to introduce Bioconductor packages for finding, accessing, and using large-scale public data resources including:
Interested students can prepare by reviewing vignettes of the packages listed in “R/Bioconductor packages used” to gain background on aspects of interest to them.
Some more general background on these resources is published in Kannan et al. (Brief. in Bioinf 2006)
Each component will include runnable examples of typical usage that students are encouraged to run during demonstration of that component.
r BiocStyle::Biocpkg("GEOquery"): Access to the NCBI Gene Expression Omnibus (GEO), a public repository of gene expression (primarily microarray) data.
r BiocStyle::Biocpkg("GenomicDataCommons"): Access to the NIH / NCI Genomic Data Commons RESTful service.
r BiocStyle::Githubpkg("seandavi/SRAdbV2"): A compilation of metadata from the NCBI Sequence Read Archive, the largest public repository of sequencing data from the next generation of sequencing platforms, and tools
r BiocStyle::Biocpkg("curatedTCGAData"): Curated data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
r BiocStyle::Biocpkg("curatedMetagenomicData"): Curated metagenomic data of the human microbiome
r BiocStyle::Biocpkg("HMP16SData"): Curated metagenomic data of the human microbiome
r BiocStyle::Biocpkg("PharmacoGx"): Curated large-scale preclinical pharmacogenomic data and basic analysis tools
This is a 55m workshop. Working through all the materials will take longer than this, but this short period will provide an overview and chance to ask questions about the content.
|Q & A.||25m|
Bioconductor provides access to significant amounts of publicly available experimental data. This workshop introduces students to Bioconductor interfaces to the NCBI’s Gene Expression Omnibus, Genomic Data Commons, Sequence Read Archive and PharmacoDB. It additionally introduces curated resources providing The Cancer Genome Atlas, the Human Microbiome Project and other microbiome studies, and major pharmacogenomic studies, as native Bioconductor objects ready for analysis and comparison to in-house datasets.