- Add 3-way comparisons
- Incorporate motif detection
- Checks for input file consistency/structure
- Add Jon Bischlak's install of R4.2.0
- Update manual to include all recent changes
- Add
pairwise_comparisons/{t1}_{t2}/{t1}_{ref1}_{treat1}_{t2}_{ref2}_{treat2}-de_genes.csvto output of pairwise_comparisons when RNA-Seq data is provided - Find & fix all hacks related to name errors in
plyranges/extraChIPscoercion & old package versions - Cleanup handling of detected genes, particularly in the setup of annotations