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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "edgeR" in publications use:'
type: software
title: 'edgeR: Empirical Analysis of Digital Gene Expression Data in R'
version: 4.3.16
doi: 10.1101/2024.01.21.576131
identifiers:
- type: doi
  value: 10.32614/CRAN.package.edgeR
- type: url
  value: https://bioconductor.org/packages/edgeR
abstract: 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.
authors:
- family-names: Chen
  given-names: Yunshun
  email: yuchen@wehi.edu.au
- family-names: Lun
  given-names: Aaron TL
- family-names: McCarthy
  given-names: Davis J
- family-names: Chen
  given-names: Lizhong
- family-names: Baldoni
  given-names: Pedro
- family-names: Ritchie
  given-names: Matthew E
- family-names: Phipson
  given-names: Belinda
- family-names: Hu
  given-names: Yifang
- family-names: Zhou
  given-names: Xiaobei
- family-names: Robinson
  given-names: Mark D
- family-names: Smyth
  given-names: Gordon K
preferred-citation:
  type: article
  title: 'edgeR 4.0: powerful differential analysis of sequencing data with expanded
    functionality and improved support for small counts and larger datasets'
  authors:
  - family-names: Chen
    given-names: Yunshun
    email: yuchen@wehi.edu.au
  - family-names: Chen
    given-names: Lizhong
  - family-names: Lun
    given-names: Aaron T L
  - family-names: Baldoni
    given-names: Pedro
  - family-names: Smyth
    given-names: Gordon K
  year: '2024'
  journal: bioRxiv
  doi: 10.1101/2024.01.21.576131
repository: https://bioc.r-universe.dev
commit: ab7fbb6f7976c30d087b21c5bcdbe7c2a1b13ef0
url: https://bioinf.wehi.edu.au/edgeR/
date-released: '2024-09-21'
contact:
- family-names: Chen
  given-names: Yunshun
  email: yuchen@wehi.edu.au
references:
- type: article
  title: 'From reads to genes to pathways: differential expression analysis of RNA-Seq
    experiments using Rsubread and the edgeR quasi-likelihood pipeline'
  authors:
  - family-names: Chen
    given-names: Yunshun
  - family-names: Lun
    given-names: Aaron T L
  - family-names: Smyth
    given-names: Gordon K
  year: '2016'
  journal: F1000Research
  volume: '5'
  doi: 10.12688/f1000research.8987.2
  start: '1438'
- type: article
  title: Differential expression analysis of multifactor RNA-Seq experiments with
    respect to biological variation
  authors:
  - family-names: McCarthy
    given-names: Davis J
  - family-names: Chen
    given-names: Yunshun
  - family-names: Smyth
    given-names: Gordon K
  year: '2012'
  journal: Nucleic Acids Research
  volume: '40'
  issue: '10'
  doi: 10.1093/nar/gks042
  start: 4288-4297
- type: article
  title: 'edgeR: a Bioconductor package for differential expression analysis of digital
    gene expression data'
  authors:
  - family-names: Robinson
    given-names: Mark D
  - family-names: McCarthy
    given-names: Davis J
  - family-names: Smyth
    given-names: Gordon K
  journal: Bioinformatics
  volume: '26'
  issue: '1'
  year: '2010'
  doi: 10.1093/bioinformatics/btp616
  start: 139-140