edgeR protocols

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chevron_left Normalization Gene set enrichment analysis Differential expression DGE analysis Differential abundant feature detection Differential expression detection Time course Batch effect correction chevron_right
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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 3.22.4
Stability Stable
Requirements
AnnotationDbi, methods, stats, graphics, splines, utils, R(>=2.15.0), locfit, Rcpp, org.Hs.eg.db, readr, limma(>=3.34.5)
Maintained Yes

Subtool


  • calcNormFactors

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Versioning


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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

 (894)
2018
PMCID: 5752201
PMID: 29297464
DOI: 10.7554/eLife.29815.043

[…] () with default parameters against ensembl’s matching gtf file for ef4.72 and aggregated on the gene-level. the workflow is summarized in ., analysis of p-body associated mrnas was performed using edger versions 3.0 and 3.12.1 (rrid:scr_012802) () using standard procedures for count normalization and estimation of dispersion. the gel label and batch were included as factors in the experimental […]

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 []. 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

[…] sample using the “summarizeoverlaps” function []. 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 [] 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: 5761948
PMID: 29320567
DOI: 10.1371/journal.pone.0190987

[…] quality reads (phred score < 10) were eliminated using picard tool (http://picard.sourceforge.net/; version 1.83) and only unique reads were considered for gene expression level estimation. the edger method (version 3.2.4), was applied for analysis of differential expression between conditions []. this software allows normalization of rna-seq data based on sequencing depth, gc content, […]

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 […]


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edgeR in publications

 (3253)
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] of data. for the analysis of histone mark intensities in genes, mapped reads per gene were counted with featurecounts (1.5.0), respective input counts subtracted, and normalized via tmm using the edger package. the pearson correlation coefficient between changes in respective histone marks over gene bodies after setd2 knockdown was calculated with the functions bigwigcompare, […]

PMCID: 5958096
PMID: 29773799
DOI: 10.1038/s41467-018-04398-z

[…] to rna-seq following a procedure we recently described. the existence of differential gene expression in the medial basal hypothalamus during pubertal development was determined by employing the edger analysis package. an initial trimming and adaptor removal step was carried out using trimmomatic. removal of the illumina adapter sequences and default filtering parameters was performed […]

PMCID: 5955981
PMID: 29769661
DOI: 10.1038/s41598-018-26065-5

[…] the sequenced data from the mh-grid cohort was analysed using an r-package. we evaluated differential mirna expression between mho and mao samples. de analysis was conducted using the r library edger. the data was normalised, using the weighted trimmed mean of m-values (tmm) method, an optimal method for the normalization of count data. we estimated tagwise dispersion (specific dispersion […]

PMCID: 5955895
PMID: 29769602
DOI: 10.1038/s41598-018-26035-x

[…] identified and labelled. next, differential expression analyses between lean and obese animals at each time point were performed at both the gene and transcript levels using the bioconductor package edger. the numbers of differentially expressed genes and differentially expressed transcripts from this analysis are summarized in table . in concordance with the gene-level analyses, the number […]

PMCID: 5953949
PMID: 29765016
DOI: 10.1038/s41467-018-04234-4

[…] uniquely overlap gene exons using r/bioconductor (v.3.2.3) and the “summarizeoverlaps” function of the genomicalignments package (v1.6.3). differentially expressed genes (degs) were determined using edger (v3.12.1), where a benjamini–hochberg fdr ≤0.05 and a twofold change in expression was required for significance. only genes expressed at more than 1 fpkm in at least two samples […]


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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.