TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
☆119Jan 8, 2026Updated 4 months ago
Alternatives and similar repositories for hickit
Users that are interested in hickit are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Tools to analyze Dip-C (or other 3C/Hi-C) data☆76Mar 28, 2026Updated last month
- Particle dynamics and simulated annealing for chromosome structure calculation☆30Mar 15, 2024Updated 2 years ago
- Chromatin contact paired-read single-cell Hi-C processing module for Nuc3D and NucTools☆15Sep 15, 2025Updated 8 months ago
- Fast alignment and preprocessing of chromatin profiles☆220Mar 20, 2026Updated 2 months ago
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆92Jan 28, 2025Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆78Jul 22, 2025Updated 10 months ago
- A cool place to store your Hi-C☆237Updated this week
- A modular Hi-C mapping pipeline☆103Dec 5, 2024Updated last year
- Preprocessing paired-end reads produced with experiment-specific protocols☆32Jun 28, 2018Updated 7 years ago
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆81Oct 31, 2024Updated last year
- A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes☆76Oct 21, 2023Updated 2 years ago
- Python reimplementation of hicrep with compatibility for sparse matrices☆19Dec 18, 2022Updated 3 years ago
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆437Mar 28, 2024Updated 2 years ago
- A collection of tools for Hi-C data analysis☆643Updated this week
- 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.
- Extract 3D contacts (.pairs) from sequencing alignments☆132Feb 3, 2026Updated 3 months ago
- “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau☆190Jul 13, 2020Updated 5 years ago
- Particle dynamics and simulated annealing for chromosome structure calculation☆18Jan 17, 2018Updated 8 years ago
- ☆73Nov 21, 2025Updated 6 months ago
- QC report generator for Hi-C pairs file☆13Sep 14, 2020Updated 5 years ago
- Scripts for HiRES analysis☆14Jul 26, 2024Updated last year
- HiC for copy Number variation and Translocation detection☆41Aug 4, 2021Updated 4 years ago
- Notes on single-cell Hi-C technologies, tools, and data☆89Feb 28, 2026Updated 2 months ago
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆482Aug 31, 2025Updated 8 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆71Dec 16, 2022Updated 3 years ago
- Pore-C support☆54Feb 22, 2023Updated 3 years ago
- ☆32Sep 28, 2019Updated 6 years ago
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆272Jul 17, 2025Updated 10 months ago
- A toolkit for analyzing architectural stripes☆22Dec 1, 2024Updated last year
- Software to assemble contigs/scaffolds into chromosomes using Hi-C data☆29Sep 26, 2024Updated last year
- ☆78Jun 12, 2020Updated 5 years ago
- Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.☆210May 19, 2018Updated 8 years ago
- A Hi-C scaffolding method☆22Dec 22, 2021Updated 4 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.
- Hi-C data analysis tool☆13May 31, 2017Updated 8 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
- Visualization and analysis software for Hi-C data -☆295Aug 6, 2024Updated last year
- SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances☆93Jan 26, 2023Updated 3 years ago
- The tools for your .cool's☆164Mar 19, 2026Updated 2 months ago
- Repository for signature genes from Immune Cell Atlas☆20Sep 25, 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…☆111Nov 12, 2025Updated 6 months ago