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variancePartition specifications

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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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Versioning


No version available

Documentation


Maintainer


  • person_outline Gabriel Hoffman <>

Publications for variancePartition

variancePartition citations

 (6)
library_books

Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

2018
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 […]

library_books

Neighbourhood interactions drive overyielding in mixed species tree communities

2018
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 […]

library_books

Transcriptional signatures of schizophrenia in hiPSC derived NPCs and neurons are concordant with post mortem adult brains

2017
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. […]

library_books

Integrative transcriptomic analysis reveals key drivers of acute peanut allergic reactions

2017
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 […]

library_books

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

2017
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 […]

library_books

Parallel changes in serum proteins and diffusion tensor imaging in methamphetamine associated psychosis

2017
PMCID: 5333148
PMID: 28252112
DOI: 10.1038/srep43777

[…] component analysis to identify potential outliers outside two standard deviations from these averages; no outliers were present in these data. finally, linear mixed models from the r package variancepartition were used to characterize and identify environmental drivers that may affect the observed protein abundances between groups. this approach quantifies variation in each abundance […]


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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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