voom specifications

Information


Unique identifier OMICS_15212
Name voom
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
Stability Stable
Requirements limma, edgeR, baySeq, DESeq, DSS, PoissonSeq, tweeDEseqCountData
Source code URL http://bioinf.wehi.edu.au/voom/Simulation_Full.R
Maintained Yes

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Maintainer


  • person_outline Gordon Smyth <>

voom article

voom citations

 (3)
2018
PMCID: 5856766

[…] in cufflinks46, and filtering for long non-coding genes and pairwise differential expression analysis performed in cuffdiff46. data from female mice were analyzed as per hodes et al. 5 whereby the voom47 and limma48 packages were utilized to generate differential expression signatures. for both sexes, differential expression comparisons were generated to compare the effects of esr1 […]

2015
PMCID: 4538839

[…] package) was used to conduct de analyses. limma utilizes a standard variance moderated across all genes using a bayesian model and produces p-values with greater degrees of freedom (55). the voom module was used to transform the data based on observational level weights derived from the mean-variance relationship prior to statistical modeling (56) (supplementary figure s2). experimental […]

2015
PMCID: 4427321

[…] between differential co-expression and differential expression, we compared the two measures for metabolic genes in brca and kirc (fig 3). we assessed differential expression using the limma voom package [37]. we found that the magnitude of differential expression (as quantified by the log2 ratio of tumor to normal expression) was weakly associated with the frequency of differential […]

voom institution(s)
Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia; Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria, Australia; Department of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia

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