Tools & Resources

Useful learning resources, especially for R and Github:

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.

ffpe and ffpeExampleData Bioconductor packages: Quality assessment and control for FFPE microarray expression data.

pensim R package: Simulation of high-dimensional data and parallelized repeated penalized regression.