edgeR pipeline

edgeR specifications

Information


Unique identifier OMICS_01308
Name edgeR
Alternative name empirical analysis of DGE in R
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.22.3
Stability Stable
Requirements limma
Maintained Yes

Subtool


  • calcNormFactors

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Versioning


Add your version

Documentation


Maintainer


  • person_outline Mark Robinson <>

Additional information


http://www.bioconductor.org/packages/release/bioc/manuals/edgeR/man/edgeR.pdf

Publications for empirical analysis of DGE in R

edgeR citations

 (108)
2018
PMCID: 5946439

[…] reference sequences (ensembl) [28] using gsnap [29]. mapped reads are quantified as raw counts in each file by xepress. differentially expressed genes were analyzed using the r-bioconductor package edger [30]. for a gene to be a differentially expressed gene (deg), it has to alter at least two fold with a false discovery rate (fdr) adjusted p-value less than 0.05 (log2fc ≥ 1 or log2fc ≤ − 1, […]

2018
PMCID: 5932758

[…] with an average expression level lower than 1 for all phenotypes in mcf7 and t-47d cells, respectively, were excluded for further analysis. differential expression (de) analysis was performed using edger [21, 22] for special group comparisons in the study. all p values were corrected by multiple testing false discovery rate (fdr) adjustments. genes with fdr < 0.05 and absolute value of fold […]

2018
PMCID: 5945544

[…] were mapped to the human transcriptome and reference genome (grch37.65/hg19) by using tophat 2.0 14 and bowtie 2.0. differential expression between the different exposures was calculated by using edger16. detailed analysis of the rna sequencing dataset will be published elsewhere after detailed analysis of gene ontology, pathway analysis and gene functional classification analysis. […]

2018
PMCID: 5874392

[…] from the r package rsubread v. 1.22.3.16 reported expression values are the observed read counts converted to counts per million mapped reads, as implemented in the cpm function from the r package edger.17 the rna-sequencing raw data file was submitted to arrayexpress and is available under accession number e-mtab-5143., array-cgh analysis of 125 beec patients did not reveal any deletions […]

2018
PMCID: 5885015

[…] using featurecounts, set to unambiguously assign uniquely aligned paired-end reads in a stranded manner to gene exon annotation [32]. differential gene expression analysis was performed using the edger bioconductor package that was customized to filter out all bovine rrna genes, genes displaying expression levels below 1 count per million (cpm) in at least ten individual libraries […]

edgeR institution(s)
Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia; Epigenetics Laboratory, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
edgeR funding source(s)
Supported by the National Health and Medical Research Council (481347- MDR, 490037-AO).

edgeR review

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Arup Ghosh

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Desktop
edgeR is a great tool for differential expression analysis using counts.