edgeR statistics

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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 3.22.4
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

Download


galaxy.png

Versioning


No version available

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

 (2986)
library_books

MLL fusion driven leukemia requires SETD2 to safeguard genomic integrity

2018
Nat Commun
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] ion 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, multiBigwigSummar […]

call_split

Elucidating the genetic architecture of reproductive ageing in the Japanese population

2018
Nat Commun
PMCID: 5958096
PMID: 29773799
DOI: 10.1038/s41467-018-04398-z
call_split See protocol

[…] cted 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 as sugg […]

library_books

Circulating MiR 374a 5p is a potential modulator of the inflammatory process in obesity

2018
Sci Rep
PMCID: 5955981
PMID: 29769661
DOI: 10.1038/s41598-018-26065-5

[…] 0.05).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 le […]

call_split

Computational identification and validation of alternative splicing in ZSF1 rat RNA seq data, a preclinical model for type 2 diabetic nephropathy

2018
Sci Rep
PMCID: 5955895
PMID: 29769602
DOI: 10.1038/s41598-018-26035-x
call_split See protocol

[…] Raw sequencing reads were processed by Salmon 0.8.2 using Ensembl v87 rat annotation with default options. The resulting isoform-level counts tables were analysed using the R/Bioconductor package edgeR 3.16.5 for normalization and differential expression between lean and obese groups at each time point. The quasi-likelihood F-test glmQLFit was used instead of a likelihood ratio test because of […]

library_books

B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation

2018
Nat Commun
PMCID: 5953949
PMID: 29765016
DOI: 10.1038/s41467-018-04234-4

[…] aks was determined and samples that did not contain 5–25% of reads in peaks were eliminated from subsequent analysis. This included one sample. Differentially accessible regions were determined using edgeR (v3.12.1) for all accessible regions, where an FDR ≤0.01 and a signal fold change ≥2 was required for significance. K-means clustering of differentially accessible regions was performed in R usi […]

library_books

Inhibition of 2 AG hydrolysis differentially regulates blood brain barrier permeability after injury

2018
PMCID: 5952841
PMID: 29759062
DOI: 10.1186/s12974-018-1166-9

[…] The read count data were normalized by the trimmed mean of the M-values method [] using the calcNormFactors() function from the edgeR package []. The mean-variance relationship of the counts was estimated using the voom() function [] from the limma package []. To identify differentially expr […]

Citations

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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.