Extract 3D contacts (.pairs) from sequencing alignments
☆133Feb 3, 2026Updated 4 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☆103Dec 5, 2024Updated last year
- A cool place to store your Hi-C☆240Jun 1, 2026Updated last week
- The tools for your .cool's☆166Mar 19, 2026Updated 2 months ago
- 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☆191Jun 1, 2026Updated last week
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆92Jan 28, 2025Updated last year
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆78Jul 22, 2025Updated 10 months ago
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated last year
- Python bindings to UCSC BigWig and BigBed library☆36Apr 6, 2026Updated 2 months ago
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆83Jan 24, 2025Updated last year
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆273Jul 17, 2025Updated 10 months ago
- Statistically Significant loops from HiChIP data☆46Apr 17, 2024Updated 2 years ago
- Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the…☆23Jun 4, 2023Updated 3 years ago
- R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes☆22May 11, 2023Updated 3 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.
- Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…☆94Aug 29, 2022Updated 3 years ago
- Cooler demo using a Jupyter notebook Binder☆19Sep 24, 2020Updated 5 years ago
- A collection of tools for Hi-C data analysis☆643May 28, 2026Updated last week
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆439Mar 28, 2024Updated 2 years ago
- Joint normalization of multiple Hi-C matrices, visualization and detection of differential chromatin interactions, supporting covariates.☆10Apr 22, 2022Updated 4 years ago
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆71Dec 16, 2022Updated 3 years ago
- Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.☆211May 19, 2018Updated 8 years ago
- An easy-to-use Hi-C data processing software supporting distributed computation.☆62Aug 6, 2024Updated last year
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆486Aug 31, 2025Updated 9 months ago
- 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.
- Red-C data processing☆15Apr 18, 2023Updated 3 years ago
- R package to evaluate the reproducibility of Hi-C data☆27Jun 23, 2023Updated 2 years ago
- FAN-C: Framework for the ANalysis of C-like data☆121Mar 13, 2024Updated 2 years ago
- snakemake pipeline for Hi-C post-processing☆22Jun 27, 2024Updated last year
- ☆18Nov 9, 2020Updated 5 years ago
- Fast, flexible and extensible genome browser.☆340May 15, 2026Updated 3 weeks ago
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 5 months ago
- Extract data quickly from Juicebox via straw☆70Apr 6, 2025Updated last year
- Fast alignment and preprocessing of chromatin profiles☆222Mar 20, 2026Updated 2 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Genome-wide contact analysis using sklearn☆75Mar 23, 2024Updated 2 years ago
- CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hie…☆27Apr 16, 2025Updated last year
- Pore-C support☆54Feb 22, 2023Updated 3 years ago
- Python bindings for hictk: read and write .cool and .hic files directly from Python☆16May 25, 2026Updated 2 weeks ago
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆42Jan 31, 2024Updated 2 years ago
- ☆36Feb 22, 2023Updated 3 years ago
- TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C☆119Jan 8, 2026Updated 5 months ago