The variancePartition R package implements a computational workflow (Fig. 1) that is complementary to standard analyses and provides particular insight into datasets with multiple dimensions of variation. variancePartition provides a user-friendly, parallelized interface for genome-wide analysis and publication quality visualizations to examine the results. Because the variance fractions are simple to describe and interpret, variancePartition can give particular insight into how each dimension of variation contributes to transcriptional variability. A typical variancePartition analysis comprises: 1) fitting a linear mixed model to quantify the contribution of each dimension of variation to each gene, 2) visualizing the results, and 3) integrating additional data about each gene to interpret drivers of this variation. The variancePartition workflow requires only a few lines of R code for pre-processing, analysis and visualization and this enables rapid interpretation of complex datasets.
