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

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Maintainer


  • person_outline Gabriel Hoffman <>

Publications for variancePartition

variancePartition in publications

 (6)
PMCID: 5859661
PMID: 29554982
DOI: 10.1186/s40168-018-0434-3

[…] principal component analysis was performed in r with vegan [] on expressed root and shoot transcripts of plants and the eukaryotic microbiome. variance partition analysis was performed in r with variancepartition [] on root expressed transcripts of plant, the eukaryotic microbiome and phialocephala., the 19 shoot samples were used for qpcr to verify rna-seq gene expression calls using […]

PMCID: 5861250
PMID: 29559628
DOI: 10.1038/s41467-018-03529-w

[…] 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., data that support the findings of this study have been deposited in the bef-china project database (http://china.befdata.biow.uni-leipzig.de/) and are available […]

PMCID: 5738408
PMID: 29263384
DOI: 10.1038/s41467-017-02330-5

[…] it is possible to (partially) correct for some variables. to decompose gene expression into the percentage attributable to multiple biological and technical sources of variation, we applied variancepartition (fig. ). for each gene we calculated the percentage of expression variation attributable to cell type, donor, diagnosis, sex, as well as ctc scores for both fibroblast sets. […]

PMCID: 5715016
PMID: 29203772
DOI: 10.1038/s41467-017-02188-7

[…] 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 […]

PMCID: 5511210
PMID: 28710498
DOI: 10.1038/s41598-017-05720-3

[…] 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 […]


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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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