A collection of tools for Hi-C data analysis
☆639Mar 22, 2026Updated 3 weeks ago
Alternatives and similar repositories for HiC_tools
Users that are interested in HiC_tools are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.☆204Feb 27, 2026Updated last month
- Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.☆208May 19, 2018Updated 7 years ago
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆269Jul 17, 2025Updated 8 months ago
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆434Mar 28, 2024Updated 2 years ago
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆479Aug 31, 2025Updated 7 months ago
- Serverless GPU API endpoints on Runpod - Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- The tools for your .cool's☆163Mar 19, 2026Updated 3 weeks ago
- FAN-C: Framework for the ANalysis of C-like data☆120Mar 13, 2024Updated 2 years ago
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆81Jan 24, 2025Updated last year
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆67Jun 7, 2019Updated 6 years ago
- “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau☆190Jul 13, 2020Updated 5 years ago
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆81Oct 31, 2024Updated last year
- A modular Hi-C mapping pipeline☆102Dec 5, 2024Updated last year
- A cool place to store your Hi-C☆234Apr 6, 2026Updated last week
- Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…☆93Aug 29, 2022Updated 3 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Genome-wide contact analysis using sklearn☆73Mar 23, 2024Updated 2 years ago
- Notes on single-cell Hi-C technologies, tools, and data☆88Feb 28, 2026Updated last month
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆78Jul 22, 2025Updated 8 months ago
- GENome Organisation Visual Analytics☆89Feb 3, 2026Updated 2 months ago
- Extract 3D contacts (.pairs) from sequencing alignments☆130Feb 3, 2026Updated 2 months ago
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated last year
- Docker for 4DN Hi-C processing pipeline☆61Nov 26, 2024Updated last year
- dcHiC: Differential compartment analysis for Hi-C datasets☆75Jan 10, 2024Updated 2 years ago
- Software to compute reproducibility and quality scores for Hi-C data☆50Apr 12, 2019Updated 7 years ago
- Serverless GPU API endpoints on Runpod - Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆92Jan 28, 2025Updated last year
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆42Jan 31, 2024Updated 2 years ago
- python module to plot beautiful and highly customizable genome browser tracks☆870Jul 10, 2024Updated last year
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Dec 16, 2022Updated 3 years ago
- Visualization and analysis software for Hi-C data -☆291Aug 6, 2024Updated last year
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph☆92Oct 29, 2025Updated 5 months ago
- R package to evaluate the reproducibility of Hi-C data☆27Jun 23, 2023Updated 2 years ago
- TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C☆116Jan 8, 2026Updated 3 months ago
- Fast alignment and preprocessing of chromatin profiles☆217Mar 20, 2026Updated 3 weeks ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Package for analysis and characterization of differential TADs☆27Apr 25, 2022Updated 3 years ago
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 3 months ago
- Software to assemble contigs/scaffolds into chromosomes using Hi-C data☆28Sep 26, 2024Updated last year
- Jupyter notebook based genomic data visualization toolkit.☆254Dec 4, 2025Updated 4 months ago
- Python library for processing and visualizing Hi-C data☆20May 31, 2020Updated 5 years ago
- Accurate and flexible loops calling tool for 3D genomic data.☆114May 19, 2022Updated 3 years ago
- A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps☆61Aug 28, 2025Updated 7 months ago