edgeR protocols

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 IN pipelines

 (393)
2018
PMCID: 5753479
PMID: 29298680
DOI: 10.1186/s12864-017-4382-2

[…] differential expression between the unisexual (p. formosa) and sexual (p. mexicana and p. latipinna) species was analyzed for gene clusters with transcripts occurring in all three species using edger [59]. because of the absence of a second (replicate) unisexual species, the dispersion value was set to 0.1 as recommended in the manual and statistical significance of inferred up- […]

2018
PMCID: 5754085
PMID: 29300744
DOI: 10.1371/journal.pone.0189185

[…] using the “summarizeoverlaps” function [23]. read counting was performed for exonic gene regions in a non-strand specific manner. the analysis of differentially expressed genes was performed by edger package [24] from bioconductor. the log2 fold change (log2fc) of expression profiles (as rpkm) was computed between the inoculated and mock inoculated plants (control); and resistant […]

2018
PMCID: 5763955
PMID: 29321057
DOI: 10.1186/s40168-017-0386-z

[…] v.2.0.11. biological qc was done with picardtools v.1.141. reads per gene feature were counted with htseq v.0.6p1. normalization was performed according to the design model with r/bioconductor edger v. 3.4.2. gene ontology analysis was performed using significantly upregulated mrnas (iav vs. mock, cutoff twofold, p < 0.05) as input for metacore (genego, thomson reuters) pathway analysis […]

2018
PMCID: 5766512
PMID: 29330490
DOI: 10.1038/s41598-017-18607-0

[…] free energy indexes (mfei) of the unannotated reads which could be mapped to bovine genome., to compare the mirna expression levels between the two samples to determine the de mirnas, the software edger was utilized to analyze the expression level of mirnas obtained from the two samples and de mirnas were screened between catlleyak and yak after the number of reads were normalized […]

2018
PMCID: 5774689
PMID: 29351308
DOI: 10.1371/journal.pone.0190933

[…] transcript catalog using cuffmerge. the comparative transcriptome studies were conducted for 16 samples from the skins of e6–e21 chicken embryos. in this study, 5830 degs were identified using edger [19]. eigengenes were calculated for each gene co-expression module in order to visualize the gene expression patterns for each module using weighted gene co-expression network analysis (wgcna) […]

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.