Extract 3D contacts (.pairs) from sequencing alignments
☆126Feb 3, 2026Updated last month
Alternatives and similar repositories for pairtools
Users that are interested in pairtools are comparing it to the libraries listed below
Sorting:
- A modular Hi-C mapping pipeline☆101Dec 5, 2024Updated last year
- A cool place to store your Hi-C☆231Updated this week
- The tools for your .cool's☆161Jul 7, 2025Updated 8 months ago
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆81Oct 31, 2024Updated last year
- Genomic interval operations on Pandas DataFrames☆190Mar 2, 2026Updated 2 weeks ago
- 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☆77Jul 22, 2025Updated 7 months ago
- Lightweight converter between hic and cool contact matrices.☆75Jul 15, 2024Updated last year
- Python bindings to UCSC BigWig and BigBed library☆36Mar 13, 2026Updated last week
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆80Jan 24, 2025Updated last year
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆268Jul 17, 2025Updated 8 months ago
- Statistically Significant loops from HiChIP data☆46Apr 17, 2024Updated last year
- Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the…☆23Jun 4, 2023Updated 2 years ago
- R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes☆21May 11, 2023Updated 2 years ago
- Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…☆92Aug 29, 2022Updated 3 years ago
- Cooler demo using a Jupyter notebook Binder☆18Sep 24, 2020Updated 5 years ago
- A collection of tools for Hi-C data analysis☆633Mar 8, 2026Updated last week
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆431Mar 28, 2024Updated last year
- Joint normalization of multiple Hi-C matrices, visualization and detection of differential chromatin interactions, supporting covariates.☆10Apr 22, 2022Updated 3 years ago
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Dec 16, 2022Updated 3 years ago
- Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.☆207May 19, 2018Updated 7 years ago
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆476Aug 31, 2025Updated 6 months ago
- An easy-to-use Hi-C data processing software supporting distributed computation.☆62Aug 6, 2024Updated last year
- Red-C data processing☆15Apr 18, 2023Updated 2 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☆122Mar 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.☆339Mar 9, 2026Updated last week
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 2 months ago
- Extract data quickly from Juicebox via straw☆69Apr 6, 2025Updated 11 months ago
- Fast alignment and preprocessing of chromatin profiles☆215Jan 17, 2026Updated 2 months ago
- Genome-wide contact analysis using sklearn☆74Mar 23, 2024Updated last year
- CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hie…☆26Apr 16, 2025Updated 11 months ago
- Pore-C support☆54Feb 22, 2023Updated 3 years ago
- Python bindings for hictk: read and write .cool and .hic files directly from Python☆16Updated this week
- ☆36Feb 22, 2023Updated 3 years ago
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆41Jan 31, 2024Updated 2 years ago
- TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C☆116Jan 8, 2026Updated 2 months ago