This package has just two functions. The first, run_DESeq_all_contrasts(), is designed to help DESeq2 users extract results for all the possible pairwise comparisons after running DESeq() on a DESeqDataSet with multiple groups to compare, as a wrapper for calling either results() or lfcShrink() iteratively. If lfcShrink() was chosen, the second function, compare_reciprocal_contrasts() can help to visualise how well
lfcShrink() was able to perform with the given data, via diagnostic plots which analyse how well the pairs of reciprocal contrasts agree (i.e. when using alternative reference groups).
You can install this package from GitHub using the following code in R (first installing devtools if necessary):
# install.packages("devtools")
devtools::install_github("kescull/mirrorCheck")
If used, please cite our paper:
Katherine Elise Scull, Kiarash Behrouzfar, Daniella Brasacchio, Enid Yi Ni Lam, Dineika Chandrananda, Paul Yeh, mirrorCheck: an R package facilitating informed use of DESeq2’s lfcShrink() function for differential gene expression analysis of clinical samples, Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf070, https://doi.org/10.1093/bioadv/vbaf070