An Optimized Nested TAD caller for Hi-C data
☆26Jun 30, 2021Updated 5 years ago
Alternatives and similar repositories for OnTAD
Users that are interested in OnTAD 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☆12Jan 18, 2021Updated 5 years ago
- TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.☆49Nov 16, 2022Updated 3 years ago
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆84Jan 24, 2025Updated last year
- GRiNCH: Graph-Regularized NMF and Clustering for Hi-C☆10Mar 15, 2024Updated 2 years ago
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 3 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.
- Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.☆55Oct 22, 2026Updated last week
- StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning☆13Oct 26, 2026Updated last week
- GENome Organisation Visual Analytics☆16Dec 24, 2021Updated 4 years ago
- DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data☆38Apr 1, 2025Updated last year
- SIP: Significant Interaction Peak caller☆17Apr 24, 2025Updated last year
- R package to evaluate reproducibility of Hi-C data☆10Mar 16, 2023Updated 3 years ago
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆82Oct 31, 2024Updated 2 years ago
- A Python implementation for BH-FDR and HiCCUPS☆55Dec 29, 2025Updated 10 months ago
- Statistically Significant loops from HiChIP data☆50Apr 17, 2024Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- GENome Organisation Visual Analytics☆91Feb 3, 2026Updated 8 months ago
- Blazing fast toolkit to work with .hic and .cool files☆49Oct 26, 2026Updated last week
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition☆23Sep 12, 2023Updated 3 years ago
- Software to compute reproducibility and quality scores for Hi-C data☆52Apr 12, 2019Updated 7 years ago
- R functions for very fast eigenvector calculation☆11Jan 18, 2023Updated 3 years 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 10 months ago
- computational tool to identify trasposable element insertions using Hi-C data☆10Sep 17, 2020Updated 6 years ago
- Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…☆96Aug 29, 2022Updated 4 years ago
- Minimal scripts to reproduce the RADICL-seq analysis of the Nature Communications manuscript☆11Jan 30, 2020Updated 6 years ago
- 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.
- A GAN-based method for Enhancing Hi-C data☆33Dec 17, 2020Updated 5 years ago
- The tools for your .cool's☆172Updated this week
- A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence☆10May 15, 2024Updated 2 years ago
- TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FAST…☆113Nov 12, 2025Updated 11 months ago
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated 2 years ago
- A cross-platform method for chromatin contact normalization☆18Dec 29, 2025Updated 10 months ago
- Genome-wide contact analysis using sklearn☆79Mar 23, 2024Updated 2 years ago
- Code and data from Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020)☆15Nov 5, 2020Updated 5 years ago
- Docker for 4DN Hi-C processing pipeline☆63Nov 26, 2024Updated last year
- 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.
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆71Sep 15, 2026Updated last month
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆68Jun 7, 2019Updated 7 years ago
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆94Jan 28, 2025Updated last year
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆44Jan 31, 2024Updated 2 years ago
- iFISH Probe Design: a Python3 package to build iFISH probes.☆12Mar 11, 2022Updated 4 years ago
- R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes☆23Sep 1, 2026Updated 2 months ago
- R package to evaluate the reproducibility of Hi-C data☆28Jun 23, 2023Updated 3 years ago