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GenomeDISCO / Genome DIfferences between Smoothed COntact maps

Assesses the similarity of a pair of contact maps obtained from chromosome capture experiments. GenomeDISCO is designed for evaluating concordance and reproducibility of chromatin contact maps obtained from chromosome conformation capture experiments. It distinguishes biological replicates from different cell types with the desired sensitivity to sequencing depth, node and edge dropout noise, changes in domain boundaries and subtle differences in distance dependence.

HIPPIE / High-throughput Identification Pipeline for Promoter Interacting Enhancer elements

A high-throughput identification pipeline for promoter interacting enhancer element to streamline the workflow from mapping raw Hi-C reads, identifying DNA-DNA interacting fragments with high confidence and quality control, detecting histone modifications and DNase hypersensitive enrichments in putative enhancer elements, to ultimately extracting possible intra- and inter-chromosomal enhancer-target gene relationships.