TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
☆118Jan 8, 2026Updated 6 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☆78Jun 24, 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 10 months ago
- Fast alignment and preprocessing of chromatin profiles☆225Mar 20, 2026Updated 4 months ago
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆92Jan 28, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆78Jul 22, 2025Updated last year
- A cool place to store your Hi-C☆241Updated this week
- Python reimplementation of hicrep with compatibility for sparse matrices☆20Dec 18, 2022Updated 3 years ago
- Preprocessing paired-end reads produced with experiment-specific protocols☆32Jun 28, 2018Updated 8 years ago
- A modular Hi-C mapping pipeline☆105Dec 5, 2024Updated last year
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆82Oct 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
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆443Mar 28, 2024Updated 2 years ago
- A collection of tools for Hi-C data analysis☆648Updated 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.
- ☆73Nov 21, 2025Updated 8 months ago
- Extract 3D contacts (.pairs) from sequencing alignments☆135Feb 3, 2026Updated 5 months ago
- “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau☆190Jul 13, 2020Updated 6 years ago
- HiC for copy Number variation and Translocation detection☆41Aug 4, 2021Updated 4 years ago
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Jul 7, 2026Updated 2 weeks ago
- Particle dynamics and simulated annealing for chromosome structure calculation☆18Jan 17, 2018Updated 8 years ago
- QC report generator for Hi-C pairs file☆13Sep 14, 2020Updated 5 years ago
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆486Aug 31, 2025Updated 10 months ago
- Notes on single-cell Hi-C technologies, tools, and data☆89Jun 29, 2026Updated 3 weeks 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.
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆275Jul 17, 2025Updated last year
- ☆32Sep 28, 2019Updated 6 years ago
- Pore-C support☆54Feb 22, 2023Updated 3 years ago
- Software to assemble contigs/scaffolds into chromosomes using Hi-C data☆29Sep 26, 2024Updated last year
- SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data☆42Jul 6, 2023Updated 3 years ago
- A toolkit for analyzing architectural stripes☆23Dec 1, 2024Updated last year
- ☆78Jun 12, 2020Updated 6 years ago
- Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.☆213May 19, 2018Updated 8 years ago
- A Hi-C scaffolding method☆22Dec 22, 2021Updated 4 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Hi-C data analysis tool☆13May 31, 2017Updated 9 years ago
- Visualization and analysis software for Hi-C data -☆301Aug 6, 2024Updated last year
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆67Jun 7, 2019Updated 7 years ago
- The tools for your .cool's☆167Mar 19, 2026Updated 4 months 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 8 months ago
- Repository for signature genes from Immune Cell Atlas☆20Sep 25, 2019Updated 6 years ago
- SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances☆94Jan 26, 2023Updated 3 years ago