hi-c

Customizable workflows based on snakemake and python for the analysis of NGS data

Fast large scale matrix visualization for the web.

Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.

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

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

A modular Hi-C mapping pipeline

Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

Lightweight converter between hic and cool contact matrices.

A 3D genome data processing tutorial for ISMB/ECCB 2017

Docker for 4DN Hi-C processing pipeline

Analysis of Chromosome Conformation Capture data (Hi-C)

Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.

GENome Organisation Visual Analytics

An easy-to-use Hi-C data processing software supporting distributed computation.

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

Identify loops from Hi-C data

Large genome reassembly based on Hi-C data, continuation of GRAAL

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Bioinformatics 2020: Graph Neural Networks for DNA Sequence Classification

Builds a docker container wrapping higlass-server and higlass-client in nginx

Simple library/pipeline to generate and handle Hi-C data.

Paired Genomic Loci Tool Suite