Blazing fast toolkit to work with .hic and .cool files
☆45Jul 20, 2026Updated this week
Alternatives and similar repositories for hictk
Users that are interested in hictk are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Python bindings for hictk: read and write .cool and .hic files directly from Python☆16Updated this week
- 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 …☆14Dec 22, 2025Updated 6 months ago
- Code associated with with the 2023 Nature Genetics Paper "Region Capture Micro-C reveals coalescence of enhancers and promoters into nest…☆12May 31, 2023Updated 3 years ago
- High-performance stochastic modeling of DNA loop extrusion interactions☆18Dec 22, 2025Updated 6 months ago
- A toolkit for analyzing architectural stripes☆22Dec 1, 2024Updated last year
- 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.
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆82Oct 31, 2024Updated last year
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 3 years ago
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆83Jan 24, 2025Updated last year
- Architectural stripe detection from 3D genome conformation data☆19Sep 15, 2025Updated 10 months ago
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆43Jan 31, 2024Updated 2 years ago
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 3 years ago
- Web-Application for the cross-visualization of HiC and ChIP-seq data.☆20Feb 17, 2026Updated 5 months ago
- python implementation of the PAGE algorithm☆24Feb 15, 2026Updated 5 months ago
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated 2 years 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.
- Scripts + resources for analyzing combinatorial Hi-C data☆32Nov 5, 2019Updated 6 years ago
- The tools for your .cool's☆167Mar 19, 2026Updated 4 months ago
- dcHiC: Differential compartment analysis for Hi-C datasets☆74Jan 10, 2024Updated 2 years ago
- a minimal, scriptable genome browser for python☆54Dec 20, 2024Updated last year
- Genome-wide contact analysis using sklearn☆76Mar 23, 2024Updated 2 years ago
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Jul 7, 2026Updated 2 weeks ago
- R package to evaluate the reproducibility of Hi-C data☆27Jun 23, 2023Updated 3 years ago
- An Optimized Nested TAD caller for Hi-C data☆26Jun 30, 2021Updated 5 years ago
- Python reimplementation of hicrep with compatibility for sparse matrices☆20Dec 18, 2022Updated 3 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆15Apr 16, 2026Updated 3 months ago
- Python bindings to UCSC BigWig and BigBed library☆36Jun 22, 2026Updated last month
- Red-C data processing☆15Apr 18, 2023Updated 3 years ago
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆78Jul 22, 2025Updated 11 months ago
- gghic makes visualization of Hi-C/-like data easily in R☆29Jan 23, 2026Updated 5 months ago
- PHi-C: deciphering Hi-C data into polymer dynamics☆11Aug 12, 2020Updated 5 years ago
- Genomic interval operations on Pandas DataFrames☆193Updated this week
- Spectral and reproducibility analysis of Hi-C contact maps☆13Mar 18, 2021Updated 5 years ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition☆21Sep 12, 2023Updated 2 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 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…☆27Apr 16, 2025Updated last year
- Pipeline to analyse ChIP-Rx data, i.e ChIP-Seq with reference exogenous genome spike-in normalization☆14Apr 11, 2026Updated 3 months ago
- Extract 3D contacts (.pairs) from sequencing alignments☆134Feb 3, 2026Updated 5 months ago
- A cool place to store your Hi-C☆241Jul 13, 2026Updated last week
- 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