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variancePartition specifications

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


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Versioning


No version available

Documentation


Maintainer


  • person_outline Gabriel Hoffman

Publications for variancePartition

variancePartition citations

 (3)
call_split

Neighbourhood interactions drive overyielding in mixed species tree communities

2018
Nat Commun
PMCID: 5861250
PMID: 29559628
DOI: 10.1038/s41467-018-03529-w
call_split 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. […]

library_books

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 […]

library_books

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 […]

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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.

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