Extract 3D contacts (.pairs) from sequencing alignments
☆138Jul 29, 2026Updated 2 months ago
Alternatives and similar repositories for pairtools
Users that are interested in pairtools 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 modular Hi-C mapping pipeline☆106Dec 5, 2024Updated last year
- The tools for your .cool's☆171Mar 19, 2026Updated 6 months ago
- A cool place to store your Hi-C☆245Updated this week
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆82Oct 31, 2024Updated last year
- Genomic interval operations on Pandas DataFrames☆196Sep 7, 2026Updated last month
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆94Jan 28, 2025Updated last year
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆79Jul 22, 2025Updated last year
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated 2 years ago
- Python bindings to UCSC BigWig and BigBed library☆37Sep 14, 2026Updated 3 weeks ago
- Statistically Significant loops from HiChIP data☆49Apr 17, 2024Updated 2 years ago
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆84Jan 24, 2025Updated last year
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆279Sep 24, 2026Updated 2 weeks ago
- Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the…☆22Sep 17, 2026Updated 3 weeks ago
- Cooler demo using a Jupyter notebook Binder☆20Sep 24, 2020Updated 6 years ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes☆23Sep 1, 2026Updated last month
- 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
- A collection of tools for Hi-C data analysis☆653Updated this week
- Python NGS Repository☆10Apr 22, 2026Updated 5 months ago
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆71Sep 15, 2026Updated 3 weeks ago
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆445Mar 28, 2024Updated 2 years ago
- Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.☆214May 19, 2018Updated 8 years ago
- Joint normalization of multiple Hi-C matrices, visualization and detection of differential chromatin interactions, supporting covariates.☆10Jul 9, 2026Updated 3 months ago
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆491Sep 15, 2026Updated 3 weeks 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.
- An easy-to-use Hi-C data processing software supporting distributed computation.☆66Jul 3, 2026Updated 3 months ago
- snakemake pipeline for Hi-C post-processing☆22Jun 27, 2024Updated 2 years ago
- Red-C data processing☆15Apr 18, 2023Updated 3 years ago
- R package to evaluate the reproducibility of Hi-C data☆28Jun 23, 2023Updated 3 years ago
- FAN-C: Framework for the ANalysis of C-like data☆120Mar 13, 2024Updated 2 years ago
- A Python implementation for BH-FDR and HiCCUPS☆55Dec 29, 2025Updated 9 months ago
- ☆19Nov 9, 2020Updated 5 years ago
- Extract data quickly from Juicebox via straw☆70Apr 6, 2025Updated last year
- Fast, flexible and extensible genome browser.☆343Jun 17, 2026Updated 3 months ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- parallelLastz: Running Lastz in parallel☆18Sep 13, 2026Updated 3 weeks ago
- ☆10Jun 9, 2026Updated 4 months ago
- Genome-wide contact analysis using sklearn☆78Mar 23, 2024Updated 2 years ago
- Fast alignment and preprocessing of chromatin profiles☆229Mar 20, 2026Updated 6 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 2 months ago
- Pore-C support☆54Feb 22, 2023Updated 3 years ago
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆44Jan 31, 2024Updated 2 years ago