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.
This is a developmental version. For stable release see Bioconductor version.
For questions about specifying contrasts with dream, see examples here.
See repo of examples from the paper.
Please help speed up bug fixes by providing a ‘minimal reproducible example’ that starts with a new R session. I recommend the reprex package to produce a GitHub-ready example that is reproducable from a fresh R session.