The variancePartition software is implemented in R and is optimized for genome-wide analysis of large-scale transcriptome profiling datasets. variancePartition uses the packages lme4 [29] foreach [32], iterators [33] and doParallel [34] to efficiently fit a linear mixed model for each gene in parallel on a multicore machine with a small memory footprint. The precision weights from limma/voom [15] are seamlessly incorporated into the analysis workflow. Built-in publication quality visualizations are implemented in ggplot2 [35]. The variancePartition software including extensive documentation is available from http://bioconductor.org/packages/variancePartition and is compatible with Bioconductor ≥v3.2 for R ≥v3.2.
