edger

Label: edgeR
Package: edgeR
Tool Type: R
Title: Empirical Analysis of Digital Gene Expression Data in R
Description: Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce read counts, including ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE and CAGE. Mark D. Robinson, Davis J. McCarthy, and Gordon K. Smyth, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics. 2010 Jan 1; 26(1): 139–140. doi: 10.1093/bioinformatics/btp616. PMCID: PMC2796818
Steps: Differential expression Normalization