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☆11Jan 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
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 3 years ago
- Statistically Significant loops from HiChIP data☆47Apr 17, 2024Updated 2 years ago
- Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.☆53Jun 17, 2025Updated last year
- 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.
- GENome Organisation Visual Analytics☆16Dec 24, 2021Updated 4 years ago
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆83Jan 24, 2025Updated last year
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 6 months ago
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆82Oct 31, 2024Updated last year
- R package to evaluate reproducibility of Hi-C data☆10Mar 16, 2023Updated 3 years ago
- GENome Organisation Visual Analytics☆92Feb 3, 2026Updated 5 months ago
- Software to compute reproducibility and quality scores for Hi-C data☆52Apr 12, 2019Updated 7 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 …☆14Dec 22, 2025Updated 7 months ago
- Blazing fast toolkit to work with .hic and .cool files☆45Updated this week
- 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.
- DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data☆37Apr 1, 2025Updated last year
- Genome-wide contact analysis using sklearn☆76Mar 23, 2024Updated 2 years ago
- Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…☆95Aug 29, 2022Updated 3 years ago
- Minimal scripts to reproduce the RADICL-seq analysis of the Nature Communications manuscript☆11Jan 30, 2020Updated 6 years ago
- A cross-platform method for chromatin contact normalization☆16Dec 29, 2025Updated 6 months ago
- A GAN-based method for Enhancing Hi-C data☆33Dec 17, 2020Updated 5 years ago
- SIP: Significant Interaction Peak caller☆17Apr 24, 2025Updated last year
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Jul 7, 2026Updated 2 weeks ago
- A toolkit for analyzing architectural stripes☆23Dec 1, 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.
- Code and data from Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020)☆15Nov 5, 2020Updated 5 years ago
- Lightweight converter between hic and cool contact matrices.☆74Jul 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…☆111Nov 12, 2025Updated 8 months ago
- Paired Genomic Loci Tool Suite☆35Nov 23, 2022Updated 3 years ago
- R package to evaluate the reproducibility of Hi-C data☆27Jun 23, 2023Updated 3 years ago
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆67Jun 7, 2019Updated 7 years ago
- R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes☆23May 11, 2023Updated 3 years ago
- iFISH Probe Design: a Python3 package to build iFISH probes.☆12Mar 11, 2022Updated 4 years ago
- FAN-C: Framework for the ANalysis of C-like data☆121Mar 13, 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.
- Docker for 4DN Hi-C processing pipeline☆61Nov 26, 2024Updated last year
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆78Jul 22, 2025Updated last year
- Extract 3D contacts (.pairs) from sequencing alignments☆135Feb 3, 2026Updated 5 months ago
- ☆19Nov 9, 2020Updated 5 years ago
- nanoNOMe (Nucleosome Occupancy and Methylome nanopore sequencing) Analysis☆20Nov 18, 2022Updated 3 years ago
- R functions for very fast eigenvector calculation☆11Jan 18, 2023Updated 3 years ago
- A machine-learning algorithm to predict CTCF-mediated long-range chromatin interactions☆17Nov 7, 2018Updated 7 years ago