Useful learning resources, especially for R and Github: http://waldronlab.github.io
Waldron lab published tools
MultiAssayExperiment Bioconductor package: Software for the integration of multi-omics experiments in Bioconductor
EnrichmentBrowser Bioconductor package: Seamless navigation through combined results of set-based and network-based enrichment analysis
curatedTCGAData Bioconductor package: Curated data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects
curatedMetagenomicData Bioconductor package: Microbial taxonomic, functional, and gene marker abundance for samples collected from different body sites.
curatedOvarianData Bioconductor package: Clinically annotated data for the ovarian cancer transcriptome.
HGNChelper R package: Identify and fix munged HGNC gene symbols.
pensim R package: Simulation of high-dimensional data and parallelized repeated penalized regression.