HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
☆276Jul 17, 2025Updated last year
Alternatives and similar repositories for HiCExplorer
Users that are interested in HiCExplorer are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆444Mar 28, 2024Updated 2 years ago
- A cool place to store your Hi-C☆243Updated this week
- A collection of tools for Hi-C data analysis☆652Jul 18, 2026Updated last month
- “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau☆190Jul 13, 2020Updated 6 years ago
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆488Aug 31, 2025Updated 11 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…☆96Aug 29, 2022Updated 4 years ago
- The tools for your .cool's☆169Mar 19, 2026Updated 5 months ago
- python module to plot beautiful and highly customizable genome browser tracks☆898Updated this week
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated 2 years ago
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆82Oct 31, 2024Updated last year
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 4 years ago
- Simple web browser to visualize HiC tracks☆19Dec 12, 2019Updated 6 years ago
- 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…☆112Nov 12, 2025Updated 9 months ago
- FAN-C: Framework for the ANalysis of C-like data☆120Mar 13, 2024Updated 2 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- GENome Organisation Visual Analytics☆92Feb 3, 2026Updated 6 months ago
- Extract 3D contacts (.pairs) from sequencing alignments☆138Jul 29, 2026Updated last month
- Genome-wide contact analysis using sklearn☆78Mar 23, 2024Updated 2 years ago
- dcHiC: Differential compartment analysis for Hi-C datasets☆74Jan 10, 2024Updated 2 years ago
- R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes☆23May 11, 2023Updated 3 years ago
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆84Jan 24, 2025Updated last year
- Software to assemble contigs/scaffolds into chromosomes using Hi-C data☆29Sep 26, 2024Updated last year
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Jul 7, 2026Updated last month
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆68Jun 7, 2019Updated 7 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- ☆23Jul 27, 2023Updated 3 years ago
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 3 years ago
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 8 months ago
- CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hie…☆28Jul 23, 2026Updated last month
- Visualization and analysis software for Hi-C data -☆303Aug 6, 2024Updated 2 years ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆180Oct 20, 2024Updated last year
- Accurate and flexible loops calling tool for 3D genomic data.☆114May 19, 2022Updated 4 years ago
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆94Jan 28, 2025Updated last year
- Jupyter notebook based genomic data visualization toolkit.☆260Updated this week
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Single-cell Hi-C data analysis toolbox☆28Aug 13, 2021Updated 5 years ago
- Software to compute reproducibility and quality scores for Hi-C data☆52Apr 12, 2019Updated 7 years ago
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆189May 17, 2024Updated 2 years ago
- Fast, flexible and extensible genome browser.☆341Jun 17, 2026Updated 2 months ago
- Extract data quickly from Juicebox via straw☆70Apr 6, 2025Updated last year
- Tools to process and analyze deep sequencing data.☆763Aug 19, 2026Updated last week
- scripts for analyzing the CVDC data.☆20Dec 5, 2019Updated 6 years ago