edgeR

edgeR is a tool for differential expression (DE) analysis of RNA-seq, ChIP-seq, CAGE, and SAGE data with biological replicates. The edgeR algorithm uses information from all the genes, computes the dispersion using a weighted likelihood and F-test techniques. For the normalization, it can use the trimmed mean of M-values, upper-quartile (UQ) procedure, Relative Log Expression (RLE), and DESeq. It can compare two groups, paired and unpaired, or use a Generalized Linear Model (GLM). The upper-quartile (UQ) procedure is also applicable to single-cell RNA-seq (scRNA-seq).

Topic

RNA-Seq;ChIP-seq

Detail

  • Operation: Differential gene expression analysis

  • Software interface: Command-line user interface

  • Language: R

  • License: GNU General Public License v>=2

  • Cost: Free

  • Version name: 3.28.0

  • Credit: National Health and Medical Research Council, Autralian Government.

  • Input: -

  • Output: -

  • Contact: Yunshun Chen yuchen@wehi.edu.au | Aaron Lun infinite.monkeys.with.keyboards@gmail.com | Mark Robinson mark.robinson@imls.uzh.ch |Gordon Smyth smyth@wehi.edu.au

  • Collection: Bioconductor

  • Maturity: -

Publications

  • Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.
  • McCarthy DJ, et al. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. 2012; 40:4288-97. doi: 10.1093/nar/gks042
  • https://doi.org/10.1093/nar/gks042
  • PMID: 22287627
  • PMC: PMC3378882

Download and documentation

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