single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
☆92Oct 29, 2025Updated 4 months ago
Alternatives and similar repositories for Higashi
Users that are interested in Higashi are comparing it to the libraries listed below
Sorting:
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition☆20Sep 12, 2023Updated 2 years ago
- ☆71Nov 21, 2025Updated 3 months ago
- Tools to analyze Dip-C (or other 3C/Hi-C) data☆74Nov 14, 2024Updated last year
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment☆21Apr 8, 2024Updated last year
- a computational tool for analyzing single cell Hi-C data☆25Apr 23, 2024Updated last year
- Single-cell Hi-C data analysis toolbox☆27Aug 13, 2021Updated 4 years ago
- Notes on single-cell Hi-C technologies, tools, and data☆87Updated this week
- SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data☆42Jul 6, 2023Updated 2 years ago
- Python bindings for hictk: read and write .cool and .hic files directly from Python☆16Updated this week
- Particle dynamics and simulated annealing for chromosome structure calculation☆28Mar 15, 2024Updated last year
- The tools for your .cool's☆160Jul 7, 2025Updated 7 months ago
- nuclear compartments, subcompartments, nuclear organization, Hi-C, autoencoder☆29Jul 5, 2024Updated last year
- A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes☆75Oct 21, 2023Updated 2 years ago
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 2 years ago
- Scripts + resources for analyzing combinatorial Hi-C data☆32Nov 5, 2019Updated 6 years ago
- DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data☆34Apr 1, 2025Updated 11 months ago
- A collection of tools for Hi-C data analysis☆631Jan 31, 2026Updated last month
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 3 years ago
- Data processing and analysis workflow for GAGE-seq, a coassay of single-cell HiC and single-cell RNA-seq☆15Oct 6, 2025Updated 4 months ago
- multiway chromatin interaction, 3D genome, single-nucleus, hypergraph representation learning☆31Jul 20, 2022Updated 3 years ago
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 2 months ago
- A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps☆61Aug 28, 2025Updated 6 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
- DiffDomain is a statistically sound method for detecting differential TADs between conditions☆17Jun 27, 2025Updated 8 months ago
- Python reimplementation of hicrep with compatibility for sparse matrices☆18Dec 18, 2022Updated 3 years ago
- R package to evaluate the reproducibility of Hi-C data☆27Jun 23, 2023Updated 2 years ago
- Blazing fast toolkit to work with .hic and .cool files☆42Feb 23, 2026Updated last week
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆77Jul 22, 2025Updated 7 months ago
- Mapping pipeline for snmC-seq based technologies.☆20Sep 25, 2023Updated 2 years ago
- Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.☆207May 19, 2018Updated 7 years ago
- ☆32Sep 28, 2019Updated 6 years ago
- 🍹This repo includes the scripts and analysis notebook for the Droplet Hi-C manuscript☆15Feb 6, 2026Updated 3 weeks ago
- Interactive visual analytic tool for exploring epigenomics data w/ associated metadata, powered by HiGlass and Gosling☆13Nov 10, 2023Updated 2 years ago
- HiC for copy Number variation and Translocation detection☆41Aug 4, 2021Updated 4 years ago
- Genome-wide contact analysis using sklearn☆72Mar 23, 2024Updated last year
- Comparison of Hi-C Experiments using Structural Similarity.☆28Jul 18, 2023Updated 2 years ago
- DECIPHER for learning high-fidelity disentangled embeddings from spatial omics data☆24Jan 20, 2026Updated last month
- Tools for DLO HiC data analyze☆16Oct 31, 2022Updated 3 years ago
- Scripts for HiRES analysis☆14Jul 26, 2024Updated last year