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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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Versioning


No version available

Maintainer


  • person_outline Gordon Smyth

Publication for voom

voom citations

 (240)
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

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

library_books

Cholesterol synthesis pathway genes in prostate cancer are transcriptionally downregulated when tissue confounding is minimized

2018
BMC Cancer
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. Only four […]

library_books

Gene expression links functional networks across cortex and striatum

2018
Nat Commun
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. […]

call_split

NKX2 5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network

2018
Nat Commun
PMCID: 5893543
PMID: 29636455
DOI: 10.1038/s41467-018-03714-x
call_split See protocol

[…] 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. Differentia […]

call_split

Genetic variation associated with increased insecticide resistance in the malaria mosquito, Anopheles coluzzii

2018
PMCID: 5885317
PMID: 29618373
DOI: 10.1186/s13071-018-2817-5
call_split See protocol

[…] ifferential expression. We further normalized individual samples using the trimmed mean of M-values (TMM) method. To estimate differential expression between genotypes and between treatments, we used voom [] in the limma package [] to perform a variance-stabilizing transformation on the raw counts and then fit a linear model using lmFit []. We applied a cell means model including genotype and trea […]

call_split

Transcriptomic profiling of nematode parasites surviving vaccine exposure

2018
PMCID: 5909036
PMID: 29534987
DOI: 10.1016/j.ijpara.2018.01.004
call_split See protocol

[…] al conclusions are not sensitive to details of the statistical methods used, we implemented two different analysis frameworks for the RNA-seq count data, using the DESeq2 v1.12.4 framework () and the voom function as implemented in the LIMMA package v3.28.21 () in R v3.3.1 (R Core Team, 2016. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, A […]

Citations

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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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