edgeR: Empirical analysis of digital gene expression data in R

A software package for the differential expression analysis of digital gene expression data, that is, of count data arising from DNA sequencing technologies. It is especially designed for differential expression analyses of RNA-Seq or SAGE data, or differential marking analyses of ChIP-Seq data.

edgeR is available as part of Bioconductor project. To install edgeR from the R command line, use the BiocManager package from CRAN:

> library("BiocManager")
> install("edgeR") 

Comprehensive documentation is distributed with the package. The edgeR User's Guide is also available from the Bioconductor edgeR package page. Help using edgeR can be obtained by posting questions or problems to the Bioconductor support site https://support.bioconductor.org.

Data Sets Used in the User's Guide

  • RNA-Seq profiles of oral carcinomas vs matched normal tissue [TuchData]
  • RNA-Seq profiles of mouse mammary gland [FuData]
  • Pasilla knockdown vs wildtype of Drosophila melanogaster [PasillaData]
  • CRISPR-Cas9 knockout screen analysis [CRISPRData]

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