variancePartition statistics
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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Versioning
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Documentation
Maintainer
- person_outline Gabriel Hoffman <>
Publications for variancePartition
VariancePartition: interpreting drivers of variation in complex gene expression studies.
variancePartition citations
(6)Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing
[…] 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 […]
Neighbourhood interactions drive overyielding in mixed species tree communities
[…] 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 […]
Transcriptional signatures of schizophrenia in hiPSC derived NPCs and neurons are concordant with post mortem adult brains
[…] 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. […]
Integrative transcriptomic analysis reveals key drivers of acute peanut allergic reactions
[…] 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 […]
Gene Network Dysregulation in Dorsolateral Prefrontal Cortex Neurons of Humans with Cocaine Use Disorder
[…] 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 […]
Parallel changes in serum proteins and diffusion tensor imaging in methamphetamine associated psychosis
[…] 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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