<br> `variancePartition` quantifies and interprets multiple sources of biological and technical variation in gene expression experiments. The package a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. The `dream()` function performs differential expression analysis for datasets with repeated measures or high dimensional batch effects. <img src="man/figures/variancePartition.png" align="center" alt="" style="padding-left:10px;" /> <br> ### Update variancePartition 1.31.1 includes a major rewrite of the backend for better error handling. See [Changelog](news/index.html). Importantly, the new version is compatible with emprical Bayes moderated t-statistics for linear mixed models using `eBayes()`. <br> ### Installation #### Latest features from GitHub ```r devtools::install_github("DiseaseNeuroGenomics/variancePartition") ``` #### Stable release from Bioconductor ```r BiocManager::install("variancePartition") ``` ### Notes This is a developmental version. For stable release see [Bioconductor version](http://bioconductor.org/packages/variancePartition/). For questions about specifying contrasts with dream, see [examples here](https://gist.github.com/GabrielHoffman/aa993222bae4d6b7d1caea2334aedbf7). See [frequently asked questions](http://bioconductor.org/packages/devel/bioc/vignettes/variancePartition/inst/doc/FAQ.html). See repo of [examples from the paper](https://github.com/GabrielHoffman/dream_analysis). ### Reporting bugs Please help speed up bug fixes by providing a 'minimal reproducible example' that starts with a new R session. I recommend the [reprex package](https://reprex.tidyverse.org) to produce a GitHub-ready example that is reproducable from a fresh R session. ## References Describes extensions of `dream` including empirical Bayes moderated t-statistics for linear mixed models and applications to single cell data - [Hoffman, et al, biorxiv (2023)](https://doi.org/10.1101/2023.03.17.533005) Describes `dream` for differential expression: - [Hoffman and Roussos, Bioinformatics (2021)](https://doi.org/10.1093/bioinformatics/btaa687) Describes the `variancePartition` package: - [Hoffman and Schadt, BMC Bioinformatics (2016)](https://doi.org/10.1186/s12859-016-1323-z)