Extract Sequence from Genome According to Annotation File

R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes

Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices

Irreproducible discovery rate for genomic interaction data

Identification of enriched motif pairs from chromatin interaction data

gghic

TAD Calling using spectral clustering in R

Identification of enriched motif pairs from chromatin interaction data

Multi-scale analysis of local differences in chromatin architecture

R package: TopDomStudy

Non-Official Fork: Integrating Multi-Track Hi-C Data for Genome-Scale Reconstruction of 3D Chromatin Structure

R package: GSE84920.parser: Parsers for the GSE84920 Hi-C Data Sets of Ramani et al. (2017)