There are 5 repositories under hi-c topic.
Customizable workflows based on snakemake and python for the analysis of NGS data
HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
Accurate and flexible loops calling tool for 3D genomic data.
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
A fast and efficient tool for converting chromatin interaction data between genome assemblies
A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.
An easy-to-use Hi-C data processing software supporting distributed computation.
Docker for 4DN Hi-C processing pipeline
Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
A Python implementation for BH-FDR and HiCCUPS
Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
A 3D genome data processing tutorial for ISMB/ECCB 2017
A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
Large genome reassembly based on Hi-C data, continuation of GRAAL
Blazing fast toolkit to work with .hic and .cool files