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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

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Maintainer


  • person_outline Mark Robinson

Publication for edgeR-robust

edgeR-robust citations

 (7)
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

[…] each 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. […]

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

[…] tRNAs were generated and the number of mapped reads to each of these bins in genome-wide manner were analyzed. We found that 15 nt bins produced the highest number of differentially expressed tRFs by edgeR robust than other bins suggesting that a predominant portion of active tRFs present in our samples are likely to be about 15 nt long. Based on this initial analysis, we decided to use 15 nt bins […]

call_split

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

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

[…] ited 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 (transcrip […]

library_books

regionReport: Interactive reports for region level and feature level genomic analyses

2016
F1000Res
PMCID: 4934510
PMID: 27429738
DOI: 10.5256/f1000research.6840.r8554

[…] ustomized general HTML report using DiffBind results with histograms instead of density plots, DESeq2 HTML and PDF reports, edgeR HTML and PDF reports using the custom ggplot2 theme theme_linedraw(), edgeR-robust HTML report, HTML report using derfinder results with the BrainSpan dataset (484 samples) and styled with knitrBootstrap, HTML report using derfinder results with the Hippo dataset (25 sa […]

library_books

Inferential considerations for low count RNA seq transcripts: a case study on the dominant prairie grass Andropogon gerardii

2016
BMC Genomics
PMCID: 4769568
PMID: 26919855
DOI: 10.1186/s12864-016-2442-7

[…] (as in extremely large counts) or a low level of expression (as in low-count transcripts) causes transcript-specific LFC estimates to shrink towards zero. In turn, the latest release of edgeR, namely edgeR robust, works by down weighting observations that deviate from the model fit [], thereby dampening the effect that observations with very high or very low expression levels have on transcript-sp […]

library_books

Evaluation of methods for differential expression analysis on multi group RNA seq count data

2015
BMC Bioinformatics
PMCID: 4634584
PMID: 26538400
DOI: 10.1186/s12859-015-0794-7

[…] urrent evaluation, researchers can easily learn what is done in TCC by comparing the corresponding original procedures described below.Two pipelines, E-E (the same as the default edgeR procedure) and edgeR_robust, were performed using the edgeR package. The E-E pipeline for analyzing count data with replicates was performed using the following functions: “DGEList”, “calcNormFactors” with the metho […]

Citations

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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].

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