Bioconductor Packages

The complete Bioconductor software ecosystem for bioinformatics in R. Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Founded in 2001, it has grown to ~3,700 packages spanning every major area of computational biology: - Gene expression analysis (DESeq2, edgeR, limma) - Single-cell analysis (SingleCellExperiment, scran, scater) - Proteomics and mass spectrometry (MSstats, OpenMS, mzR) - Flow cytometry (flowCore, flowClust) - Genomic annotation (GenomicFeatures, AnnotationDbi, biomaRt) - Sequence analysis (Biostrings, GenomicAlignments, Rsamtools) - Epigenomics (methylKit, ChIPseeker, bsseq) - Visualization (Gviz, ggbio, ComplexHeatmap) This portfolio maps each package to its upstream GitHub repository where available, falling back to the official Bioconductor mirror (github.com/bioc/*) otherwise — giving a more complete view of the authors, contributors, and development communities behind the Bioconductor ecosystem.

Created 4/16/2026 - Last updated 5/26/2026