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A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Hicexplorer ⭐ 197

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

A cool place to store your Hi-C

Accurate and flexible loops calling tool for 3D genomic data.

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

Coolpuppy ⭐ 66

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

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

Hic2cool ⭐ 50

Lightweight converter between hic and cool contact matrices.

dcHiC: Differential compartment analysis for Hi-C datasets

Hic_pipeline ⭐ 40

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

Hicpeaks ⭐ 36

A Python implementation for BH-FDR and HiCCUPS

Docker 4dn Hic ⭐ 23

Docker for 4DN Hi-C processing pipeline

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Schicexplorer ⭐ 19

Single-cell Hi-C data analysis toolbox

Genomedisco ⭐ 18

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

Hicstuff ⭐ 17

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

Hicreppy ⭐ 14

Python reimplementation of hicrep with compatibility for sparse matrices

Gcmapexplorer ⭐ 13

Genome Contact Map Explorer - gcMapExplorer. Visit:

High-performance stochastic modeling of DNA loop extrusion interactions

Hicbrowser ⭐ 11

Simple web browser to visualize HiC tracks

ViralCC: leveraging metagenomic proximity-ligation to retrieve complete viral genomes

QC report generator for Hi-C pairs file

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