edgeR-robust statistics

info info

Citations per year

info

Popular tool citations

chevron_left Differential expression chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

edgeR-robust specifications

Information


Unique identifier OMICS_03825
Name edgeR-robust
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

Download


download.png

Versioning


No version available

Maintainer


  • person_outline Mark Robinson

Publication for edgeR-robust

edgeR-robust citations

 (9)
library_books

Pharmacologic Reprogramming Designed to Induce a Warburg Effect in Porcine Fetal Fibroblasts Alters Gene Expression and Quantities of Metabolites from Conditioned Media Without Increased Cell Proliferation

2018
PMCID: 5804098
PMID: 29412741
DOI: 10.1089/cell.2017.0040

[…] sample. the differentially expressed (de) genes between sample groups, representing the culture treatment, were determined by fitting the read counts to a generalized linear model implemented in edger-robust (zhou et al., ). the false discovery rate (fdr) <0.05 was used as threshold for statistically significant differential expression of genes., without daily media changes, proliferation […]

library_books

Multifaceted functional implications of an endogenously expressed tRNA fragment in the vector mosquito Aedes aegypti

2018
PLoS Negl Trop Dis
PMCID: 5783352
PMID: 29364883
DOI: 10.1371/journal.pntd.0006186

[…] of trfs was then used to quantify the number of reads mapped to each trf in a genome-wide manner by stringtie []. to compare trf expression between different sample groups, we used the r package edger-robust [] which normalizes the read count data by using trimmed mean of m-values method (tmm), and performs statistical inference of differential expression of trfs by fitting the normalized […]

library_books

Transcriptomic response of the Antarctic pteropod Limacina helicina antarctica to ocean acidification

2017
BMC Genomics
PMCID: 5653985
PMID: 29061120
DOI: 10.1186/s12864-017-4161-0

[…] to the analysis of differential expression. differential expression of transcripts was evaluated using a negative binomial general linearized model (glm) as integrated in the bioconductor r package edger-robust []. within edger, we defined up-regulated transcripts as having a log10 fold change ≥1, and down-regulated transcripts as having a log10 fold change ≤ −1 with a false discovery rate […]

library_books

Transcriptomic profiling of purified patient derived dopamine neurons identifies convergent perturbations and therapeutics for Parkinson’s disease

2017
Hum Mol Genet
PMCID: 5409122
PMID: 28096185
DOI: 10.1093/hmg/ddw412

[…] from the joint distribution of estimates from observed counts. we performed these simulations by using the r framework nbsim developed by zhou et al. (), http://imlspenticton.uzh.ch/robinson_lab/edger_robust) et al. with following options:folddiff = 3ntags = 1000000add.outlier = trueoutliermech = “s”poutlier = 0.01drop.extreme.dispersion = 0.1, folddiff = 3, ntags = 1000000, add.outlier = […]

library_books

Uterine glands impact uterine receptivity, luminal fluid homeostasis and blastocyst implantation

2016
Sci Rep
PMCID: 5131473
PMID: 27905495
DOI: 10.1038/srep38078

[…] in the gene expression omnibus database (geo, in process)., differential expression analyses between sample groups were performed by fitting the expression data to a generalized linear model using edger-robust. differentially expressed genes (fdr p < 0.10) were further subjected to weighted correlation network analysis (using r package wgcna) to identify changes in expression modules […]

library_books

Transcription analysis of neonicotinoid resistance in Mediterranean (MED) populations of B. tabaci reveal novel cytochrome P450s, but no nAChR mutations associated with the phenotype

2015
BMC Genomics
PMCID: 4647701
PMID: 26573457
DOI: 10.1186/s12864-015-2161-5

[…] expected counts for each sample (the sum of counts in each row >10) were extracted and used for the analysis of differential expression conducted in edger-3.8.0 bioconductor package [] using edger-robust method to dampen the effect of outlier genes [] with logfc > 1 and fdr < 0.05., the expression levels of seven p450 genes found to be differentially expressed by the rna-seq […]


Want to access the full list of citations?
edgeR-robust institution(s)
Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
edgeR-robust funding source(s)
Supported by SNSF Project Grant [143883] and European Commission through the 7th Framework Collaborative Project RADIANT [305626].

edgeR-robust reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review edgeR-robust