paulsengroup / hictkView external linksLinks
Blazing fast toolkit to work with .hic and .cool files
☆42Feb 9, 2026Updated last week
Alternatives and similar repositories for hictk
Users that are interested in hictk are comparing it to the libraries listed below
Sorting:
- Python bindings for hictk: read and write .cool and .hic files directly from Python☆16Feb 2, 2026Updated 2 weeks ago
- 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 last month
- High-performance stochastic modeling of DNA loop extrusion interactions☆18Dec 22, 2025Updated last month
- python implementation of the PAGE algorithm☆20Updated this week
- gghic makes visualization of Hi-C/-like data easily in R☆24Jan 23, 2026Updated 3 weeks ago
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 2 years ago
- A toolkit for analyzing architectural stripes☆20Dec 1, 2024Updated last year
- Code associated with with the 2023 Nature Genetics Paper "Region Capture Micro-C reveals coalescence of enhancers and promoters into nest…☆12May 31, 2023Updated 2 years ago
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆79Jan 24, 2025Updated last year
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆80Oct 31, 2024Updated last year
- Architectural stripe detection from 3D genome conformation data☆18Sep 15, 2025Updated 5 months 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
- Web-Application for the cross-visualization of HiC and ChIP-seq data.☆18Nov 11, 2024Updated last year
- a minimal, scriptable genome browser for python☆53Dec 20, 2024Updated last year
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 3 years ago
- Scripts + resources for analyzing combinatorial Hi-C data☆32Nov 5, 2019Updated 6 years ago
- Python bindings to UCSC BigWig and BigBed library☆35Jan 28, 2026Updated 2 weeks ago
- R package to evaluate the reproducibility of Hi-C data☆27Jun 23, 2023Updated 2 years ago
- dcHiC: Differential compartment analysis for Hi-C datasets☆74Jan 10, 2024Updated 2 years ago
- The tools for your .cool's☆160Jul 7, 2025Updated 7 months ago
- An Optimized Nested TAD caller for Hi-C data☆25Jun 30, 2021Updated 4 years ago
- ☆16Dec 25, 2024Updated last year
- Python reimplementation of hicrep with compatibility for sparse matrices☆18Dec 18, 2022Updated 3 years ago
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated last year
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆68Dec 16, 2022Updated 3 years ago
- Genome-wide contact analysis using sklearn☆72Mar 23, 2024Updated last year
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition☆20Sep 12, 2023Updated 2 years ago
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆77Jul 22, 2025Updated 6 months ago
- trackc aims to produce beautiful genome tracks that are highly customizable☆16Jan 21, 2026Updated 3 weeks ago
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated last month
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆92Jan 28, 2025Updated last year
- Tools to analyze Dip-C (or other 3C/Hi-C) data☆74Nov 14, 2024Updated last year
- An effective alignment tool for long noisy 3C data (e.g. Pore-C and C-walk)☆14Oct 23, 2024Updated last year
- Interspecies Point Projection - A tool for comparative genomics beyond alignable sequence☆23Feb 9, 2026Updated last week
- Red-C data processing☆15Apr 18, 2023Updated 2 years ago
- pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence …☆18Jan 21, 2025Updated last year
- Spectral and reproducibility analysis of Hi-C contact maps☆13Mar 18, 2021Updated 4 years ago
- Interactive visual analytic tool for exploring epigenomics data w/ associated metadata, powered by HiGlass and Gosling☆13Nov 10, 2023Updated 2 years ago
- Fast alignment and preprocessing of chromatin profiles☆213Jan 17, 2026Updated 3 weeks ago