variancePartition statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

variancePartition specifications

Desktop

Information

Unique identifier	OMICS_13846
Name	variancePartition
Software type	Package/Module
Interface	Command line interface
Restrictions to use	None
Operating system	Unix/Linux, Mac OS, Windows
Programming languages	R
License	GNU General Public License version 2.0
Computer skills	Advanced
Version	1.10.0
Stability	Stable
Requirements	limma, methods, stats, gplots, graphics, Biobase, splines, utils, BiocStyle, grDevices, edgeR, ggplot2, DESeq2, rmarkdown, knitr, MASS, reshape2, foreach, tximport, tximportData, readr, doParallel, iterators, ballgown, dendextend, pbkrtest(>=0.4-4), colorRamps, lme4(>=1.1-10)
Maintained	Yes

Subtool

dream

Download

Versioning

No version available

Documentation

Documentation: http://bioconductor.org/packages/release/bioc/manuals/variancePartition/man/variancePartition.pdf

Maintainer

Gabriel Hoffman

Publications for variancePartition

Dream: Powerful differential expression analysis for repeated measures designs.

2018 BioRxiv

DOI: 10.1101/432567

VariancePartition: interpreting drivers of variation in complex gene expression studies

2016 BMC Bioinformatics

PMCID: 5123296

PMID: 27884101

DOI: 10.1186/s12859-016-1323-z

variancePartition citations

(3)

Neighbourhood interactions drive overyielding in mixed species tree communities

2018

Nat Commun

PMCID: 5861250

PMID: 29559628

DOI: 10.1038/s41467-018-03529-w

See protocol

[…] wed us to quantify the importance of neighbourhood interactions in driving BPRs in young tree communities.All analyses were conducted in R (version 3.3.1) using the packages lme4, lmerTest, MuMIn and variancePartition. […]

Integrative transcriptomic analysis reveals key drivers of acute peanut allergic reactions

2017

Nat Commun

PMCID: 5715016

PMID: 29203772

DOI: 10.1038/s41467-017-02188-7

[…] for each gene. Multidimensional scaling analysis was used to identify outlier RNA-seq samples, resulting in removal of one sample (Supplementary Fig. ) from the discovery cohort. In addition, we used variancePartition, to assess the contribution of technical and biological factors to variation in gene expression across the samples. This revealed minimal influence of age and gender (Supplementary F […]

Gene Network Dysregulation in Dorsolateral Prefrontal Cortex Neurons of Humans with Cocaine Use Disorder

2017

Sci Rep

PMCID: 5511210

PMID: 28710498

DOI: 10.1038/s41598-017-05720-3

[…] is analysis revealed that RIN and PMI had strong widespread effects on gene expression (p < 0.01) (Supplementary Figure ). Since the effects of one covariate could mask the effects of others, we used VariancePartition to decompose gene expression variation into the variance attributable to each covariate. We calculated the variance explained by each covariate for each gene, which confirmed the wid […]

Citations

Looking to check out a full list of citations?

variancePartition institution(s)

Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, NY, USA

variancePartition funding source(s)

Supported in part by Scientific Computing at the Icahn School of Medicine at Mount Sinai and by NIH/NHLBI U01 HL107388-04 and NIH/NIA U01 HL107388-04.

variancePartition reviews

Be the first to review variancePartition