R package to evaluate the reproducibility of Hi-C data
☆27Jun 23, 2023Updated 2 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☆42Jan 31, 2024Updated 2 years ago
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆82Jan 24, 2025Updated last year
- A pipeline for identifying conserved topologically associating domain boundaries among multiple species.☆16Jun 17, 2025Updated 10 months ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment☆21Apr 8, 2024Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Genome-wide contact analysis using sklearn☆73Mar 23, 2024Updated 2 years ago
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 3 years ago
- Simple library/pipeline to generate and handle Hi-C data.☆39Feb 13, 2026Updated 2 months ago
- R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes☆22May 11, 2023Updated 2 years ago
- Docker for 4DN Hi-C processing pipeline☆61Nov 26, 2024Updated last year
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆81Oct 31, 2024Updated last year
- Software to compute reproducibility and quality scores for Hi-C data☆51Apr 12, 2019Updated 7 years ago
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 4 months ago
- Analyzing Hi-C data in R with HiCExperiment objects☆16Updated this week
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- DiffDomain is a statistically sound method for detecting differential TADs between conditions☆18Jun 27, 2025Updated 10 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
- Micro-C QC and data analysis☆16Aug 1, 2023Updated 2 years 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
- Package for analysis and characterization of differential TADs☆27Apr 25, 2022Updated 4 years ago
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆71Dec 16, 2022Updated 3 years ago
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆92Jan 28, 2025Updated last year
- 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 4 months ago
- GENome Organisation Visual Analytics☆90Feb 3, 2026Updated 2 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆78Jul 22, 2025Updated 9 months ago
- code associated with crane-nature-2015, 10.1038/nature14450☆36Aug 28, 2015Updated 10 years ago
- FAN-C: Framework for the ANalysis of C-like data☆120Mar 13, 2024Updated 2 years ago
- ☆23Jul 27, 2023Updated 2 years ago
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated last year
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition☆20Sep 12, 2023Updated 2 years ago
- HiCDCPlus☆19Jun 6, 2022Updated 3 years ago
- Blazing fast toolkit to work with .hic and .cool files☆44Updated this week
- Pipeline for generating reference and perturbed sequences for input into predictive models.☆11Nov 15, 2024Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Extract 3D contacts (.pairs) from sequencing alignments☆131Feb 3, 2026Updated 2 months ago
- A Python implementation of the original DI domain caller☆13Aug 2, 2020Updated 5 years ago
- Tools to analyze Dip-C (or other 3C/Hi-C) data☆76Mar 28, 2026Updated last month
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 2 years ago
- Orchestrating Hi-C analysis with Bioconductor☆11Jul 11, 2025Updated 9 months ago
- A toolkit for analyzing architectural stripes☆20Dec 1, 2024Updated last year
- Super-resolution chromatin tracing 2018☆18Nov 7, 2020Updated 5 years ago