Single-cell Hi-C data analysis toolbox
☆28Aug 13, 2021Updated 5 years ago
Alternatives and similar repositories for scHiCExplorer
Users that are interested in scHiCExplorer are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Fontanka is a set of tools to work with fountains in Hi-C data. It aims to provide a flexible Python API and specialized CLI for calling …☆13Dec 22, 2025Updated 10 months ago
- ☆74Nov 21, 2025Updated 11 months ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph☆98Oct 29, 2025Updated last year
- Notes on single-cell Hi-C technologies, tools, and data☆89Jun 29, 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…☆113Nov 12, 2025Updated 11 months ago
- 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 computational tool for analyzing single cell Hi-C data☆27Apr 23, 2024Updated 2 years ago
- ☆19Mar 8, 2023Updated 3 years ago
- Explore the Hi-Cs☆12Jul 25, 2026Updated 3 months ago
- Code to reproduce analyses in Kim et al. 2025☆10Dec 17, 2025Updated 10 months ago
- ☆11Aug 30, 2021Updated 5 years ago
- ☆12Dec 21, 2021Updated 4 years ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment☆21Apr 8, 2024Updated 2 years ago
- General analysis of HiC data, including compartment A/B, domains and loops.☆14Feb 17, 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
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- TADsplimer☆10Jun 24, 2021Updated 5 years ago
- ☆13Jul 26, 2022Updated 4 years ago
- Architectural stripe detection from 3D genome conformation data☆18Sep 15, 2025Updated last year
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated 2 years ago
- HiCorr: a Hi-C data bias-correction pipeline☆31Apr 1, 2025Updated last year
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆78Jul 22, 2025Updated last year
- Tools to analyze Dip-C (or other 3C/Hi-C) data☆79Jun 24, 2026Updated 4 months ago
- Scripts + resources for analyzing combinatorial Hi-C data☆32Nov 5, 2019Updated 6 years ago
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 4 years 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.
- ☆31Sep 28, 2019Updated 7 years ago
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆281Updated this week
- 🍹This repo includes the scripts and analysis notebook for the Droplet Hi-C manuscript☆19Feb 6, 2026Updated 8 months ago
- HiSV: a computational pipeline for structural variation detection from Hi-C data☆17Jun 20, 2025Updated last year
- TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C☆122Jan 8, 2026Updated 9 months ago
- Red-C data processing☆14Apr 18, 2023Updated 3 years ago
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆71Sep 15, 2026Updated last month
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition☆23Sep 12, 2023Updated 3 years ago
- ☆14Jan 20, 2026Updated 9 months 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.
- Software to assemble contigs/scaffolds into chromosomes using Hi-C data☆29Sep 26, 2024Updated 2 years ago
- A python package to predict CRISPR-Cas PAMs☆11May 3, 2023Updated 3 years ago
- Readability enhancement tool for bioinformatics data file format☆29Jan 9, 2020Updated 6 years ago
- Slides and demos from our SciPyConf 2019 talk☆13Sep 28, 2021Updated 5 years ago
- A Python implementation for BH-FDR and HiCCUPS☆55Dec 29, 2025Updated 10 months ago
- A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes☆78Oct 21, 2023Updated 3 years ago
- DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data☆38Apr 1, 2025Updated last year