Extract Sequence from Genome According to Annotation File

gghic makes visualization of Hi-C/-like data easily in R

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

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

Irreproducible discovery rate for genomic interaction data

Identification of enriched motif pairs from chromatin interaction data

TAD Calling using spectral clustering in R

Identification of enriched motif pairs from chromatin interaction data

Analysis code for the whale shark genome project

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)

Multi-scale analysis of local differences in chromatin architecture