voom protocols

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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 <>

Publication for voom

voom in pipelines

 (54)
2018
PMCID: 5812937
PMID: 29269498
DOI: 10.1128/AEM.02294-17

[…] using the r functions binom.test and fligner.test. the r function p.adjust was used for bonferroni's correction of p values for multiple testing., the normalized and filtered data sets were voom transformed () to consider the differences in count sizes (or sequencing depth) and the overall data set variability. this was followed by differential expression analysis (dea) with an adjusted […]

2018
PMCID: 5831037
PMID: 29489876
DOI: 10.1371/journal.pone.0192947

[…] of raw library sizes applying the ‘tmm’ method that uses the weighted trimmed means of log-ratios (with respect to the reference) []. these factors were then used to normalise the data by the voom function [] (limma package, v3.26.9 []). this process of normalisation was completed in two steps: firstly, for the purpose of identifying genes with low counts (all genes with a mean expression […]

2018
PMCID: 5856766
PMID: 29549264
DOI: 10.1038/s41467-018-03567-4

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

2018
PMCID: 5864071
PMID: 29529020
DOI: 10.1371/journal.pbio.2004328

[…] factors of unwanted variation estimated using the r package ruv []—were used to account for life cycle and other unwanted batch effects. differential expression testing was conducted using the limma/voom pipeline [,]. the impact of including these covariates in the model is evident in the principal component analysis (pca) plots (, ). the choice of covariates strikes a balance between testing […]

2018
PMCID: 5873924
PMID: 29487188
DOI: 10.1534/g3.118.200022

[…] with blocks shorter than 8bps were removed. read counts were computed using rackj (http://rackj.sourceforge.net/) and normalized into log-count-per-million (logcpm) using the tmm method () and the voom method (). logcpm values were then transformed into rpkm values. differentially expressed genes were identified using t-tests on aforementioned rpkm values if the p-value was less than 0.01 […]


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voom in publications

 (216)
PMCID: 5952841
PMID: 29759062
DOI: 10.1186/s12974-018-1166-9

[…] 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 expressed genes, the log2 fold differences and p values were estimated by fitting a linear model for each gene and applying […]

PMCID: 5934875
PMID: 29724161
DOI: 10.1186/s12864-018-4719-5

[…] were removed prior to differential expression (de) analysis []. a tmm (trimmed mean of m-values) normalization was applied to all samples using edger []. after data were log2-transformed, limma-voom method (bioconductor packages) was used to conduct de analyses [, ]. the applied statistical model included time as fixed effect and animal as random effect. differentially expressed genes (deg) […]

PMCID: 5922022
PMID: 29703166
DOI: 10.1186/s12885-018-4373-y

[…] the hg19 transcriptome using tophat2 [], and featurecounts [] were used to assign the reads mapping to each gene. normalization of gene counts were performed using the normalization formula from the voom program []. gene expression and metadata from sboner [] were downloaded from geo with accession gse16560. probes were matched to gene names using the gpl5474 reference available at geo. […]

PMCID: 5897339
PMID: 29651138
DOI: 10.1038/s41467-018-03811-x

[…] nacc; thus, this region was selected to correspond to the limbic striatum. differential expression for the gtex limbic striatum (i.e., nacc), relative to the caudate and putamen was calculated using voom, controlling for age, sex, sequencing platform, and a set 15 covariates derived by nih gtex using the probablistic estimates of expression residuals method., a total of 10,616 genes unique […]

PMCID: 5893543
PMID: 29636455
DOI: 10.1038/s41467-018-03714-x

[…] gene annotation (hg19). lowly expressed genes were filtered out (less than one count per million in fewer than three samples), leaving 14,458 genes for further analysis. the data was tmm normalized, voom transformed, and differential expression assessed using empirical bayes moderated t-tests from the r bioconductor limma package. design matrix included factor for day of cell sorting. […]


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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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