HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
☆268Jul 17, 2025Updated 8 months ago
Alternatives and similar repositories for HiCExplorer
Users that are interested in HiCExplorer are comparing it to the libraries listed below
Sorting:
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆431Mar 28, 2024Updated last year
- A cool place to store your Hi-C☆231Updated this week
- A collection of tools for Hi-C data analysis☆633Mar 8, 2026Updated last week
- “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau☆189Jul 13, 2020Updated 5 years ago
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆476Aug 31, 2025Updated 6 months ago
- Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…☆92Aug 29, 2022Updated 3 years ago
- The tools for your .cool's☆161Jul 7, 2025Updated 8 months ago
- python module to plot beautiful and highly customizable genome browser tracks☆867Jul 10, 2024Updated last year
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆81Oct 31, 2024Updated last year
- Lightweight converter between hic and cool contact matrices.☆75Jul 15, 2024Updated last year
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 3 years ago
- Simple web browser to visualize HiC tracks☆19Dec 12, 2019Updated 6 years ago
- FAN-C: Framework for the ANalysis of C-like data☆122Mar 13, 2024Updated 2 years ago
- GENome Organisation Visual Analytics☆86Feb 3, 2026Updated last month
- 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 FAST…☆109Nov 12, 2025Updated 4 months ago
- Extract 3D contacts (.pairs) from sequencing alignments☆126Feb 3, 2026Updated last month
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆80Jan 24, 2025Updated last year
- Genome-wide contact analysis using sklearn☆74Mar 23, 2024Updated last year
- R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes☆21May 11, 2023Updated 2 years ago
- Software to assemble contigs/scaffolds into chromosomes using Hi-C data☆28Sep 26, 2024Updated last year
- dcHiC: Differential compartment analysis for Hi-C datasets☆74Jan 10, 2024Updated 2 years ago
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆67Jun 7, 2019Updated 6 years ago
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Dec 16, 2022Updated 3 years ago
- ☆22Jul 27, 2023Updated 2 years ago
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 2 years ago
- CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hie…☆26Apr 16, 2025Updated 11 months ago
- HiC for copy Number variation and Translocation detection☆41Aug 4, 2021Updated 4 years ago
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 2 months ago
- Visualization and analysis software for Hi-C data -☆288Aug 6, 2024Updated last year
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆178Oct 20, 2024Updated last year
- Accurate and flexible loops calling tool for 3D genomic data.☆114May 19, 2022Updated 3 years ago
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆92Jan 28, 2025Updated last year
- Jupyter notebook based genomic data visualization toolkit.☆253Dec 4, 2025Updated 3 months ago
- Single-cell Hi-C data analysis toolbox☆27Aug 13, 2021Updated 4 years ago
- Software to compute reproducibility and quality scores for Hi-C data☆50Apr 12, 2019Updated 6 years ago
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆188May 17, 2024Updated last year
- Fast, flexible and extensible genome browser.☆339Mar 9, 2026Updated last week
- Tools to process and analyze deep sequencing data.☆752Jul 23, 2025Updated 7 months ago
- Extract data quickly from Juicebox via straw☆69Apr 6, 2025Updated 11 months ago