- SICER (Spatial-clustering Identification of ChIP-Enriched Regions) for ChIP-Seq data analysis. [Package] [Publication] [Protocol].
- Lollipop for the prediction of CTCF-mediated chromatin interaction network using functional genomic features. [Package][Publication]
- IRTools for quantitative analysis of intron retention. [Package]
- HicHub for detection of hubs of interaction changes between two conditions. [Package][Publication]