R package to evaluate the reproducibility of Hi-C data
☆27Jun 23, 2023Updated 3 years ago
Alternatives and similar repositories for hicrep
Users that are interested in hicrep are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 years 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 pipeline for identifying conserved topologically associating domain boundaries among multiple species.☆17Jun 17, 2025Updated last year
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆83Jan 24, 2025Updated last year
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment☆21Apr 8, 2024Updated 2 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.
- Genome-wide contact analysis using sklearn☆76Mar 23, 2024Updated 2 years ago
- A cross-platform method for chromatin contact normalization☆16Dec 29, 2025Updated 6 months ago
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 3 years ago
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 6 months ago
- Simple library/pipeline to generate and handle Hi-C data.☆42May 18, 2026Updated 2 months ago
- R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes☆23May 11, 2023Updated 3 years ago
- Docker for 4DN Hi-C processing pipeline☆61Nov 26, 2024Updated last year
- Analyzing Hi-C data in R with HiCExperiment objects☆16Apr 29, 2026Updated 2 months ago
- Software to compute reproducibility and quality scores for Hi-C data☆52Apr 12, 2019Updated 7 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.
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆82Oct 31, 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…☆27Apr 16, 2025Updated last year
- DiffDomain is a statistically sound method for detecting differential TADs between conditions☆18Jun 27, 2025Updated last year
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Jul 7, 2026Updated 2 weeks ago
- A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes☆76Oct 21, 2023Updated 2 years ago
- Micro-C QC and data analysis☆17Aug 1, 2023Updated 2 years ago
- Package for analysis and characterization of differential TADs☆27Jul 15, 2026Updated last week
- GENome Organisation Visual Analytics☆92Feb 3, 2026Updated 5 months ago
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆92Jan 28, 2025Updated last year
- 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.
- 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 7 months ago
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆78Jul 22, 2025Updated last year
- FAN-C: Framework for the ANalysis of C-like data☆121Mar 13, 2024Updated 2 years ago
- ☆23Jul 27, 2023Updated 2 years ago
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated 2 years ago
- code associated with crane-nature-2015, 10.1038/nature14450☆38Aug 28, 2015Updated 10 years ago
- HiCDCPlus☆19Jun 6, 2022Updated 4 years ago
- Super-resolution chromatin tracing 2018☆19Nov 7, 2020Updated 5 years ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition☆21Sep 12, 2023Updated 2 years 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.
- Blazing fast toolkit to work with .hic and .cool files☆45Updated this week
- Tools to analyze Dip-C (or other 3C/Hi-C) data☆78Jun 24, 2026Updated 3 weeks ago
- Pipeline for generating reference and perturbed sequences for input into predictive models.☆12Nov 15, 2024Updated last year
- Extract 3D contacts (.pairs) from sequencing alignments☆134Feb 3, 2026Updated 5 months ago
- Orchestrating Hi-C analysis with Bioconductor☆11Jul 11, 2025Updated last year
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 3 years ago
- A reference panel guided topological structure annotation of Hi-C data☆10Mar 23, 2023Updated 3 years ago