Jupyter notebook based genomic data visualization toolkit.
☆260Aug 25, 2026Updated this week
Alternatives and similar repositories for CoolBox
Users that are interested in CoolBox are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- python module to plot beautiful and highly customizable genome browser tracks☆898Updated this week
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Jul 7, 2026Updated last month
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 4 years ago
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆84Jan 24, 2025Updated last year
- 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.
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆82Oct 31, 2024Updated last year
- FAN-C: Framework for the ANalysis of C-like data☆120Mar 13, 2024Updated 2 years ago
- The tools for your .cool's☆169Mar 19, 2026Updated 5 months ago
- Genome-wide contact analysis using sklearn☆78Mar 23, 2024Updated 2 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 8 months ago
- A toolkit for analyzing architectural stripes☆23Dec 1, 2024Updated last year
- Plotting average TAD heatmap for Hi-C data (give TAD segmentation and cool/hiclib interactions map).☆10Jun 5, 2021Updated 5 years ago
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆276Jul 17, 2025Updated last year
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 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.
- Intervene: a tool for intersection and visualization of multiple genomic region and gene sets☆151Oct 28, 2023Updated 2 years ago
- genes and genomes at your fingertips☆410Jun 9, 2026Updated 2 months ago
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆79Jul 22, 2025Updated last year
- A collection of tools for Hi-C data analysis☆652Jul 18, 2026Updated last month
- A python extension for quick access to bigWig and bigBed files☆250Jul 22, 2026Updated last month
- Performant Pythonic GenomicRanges☆492Apr 23, 2026Updated 4 months ago
- Extract 3D contacts (.pairs) from sequencing alignments☆138Jul 29, 2026Updated last month
- Genomic interval operations on Pandas DataFrames☆195Aug 3, 2026Updated 3 weeks ago
- Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.☆214May 19, 2018Updated 8 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.
- A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes☆77Oct 21, 2023Updated 2 years ago
- Package for analysis and characterization of differential TADs☆27Aug 21, 2026Updated last week
- Particle dynamics and simulated annealing for chromosome structure calculation☆30Mar 15, 2024Updated 2 years ago
- dcHiC: Differential compartment analysis for Hi-C datasets☆74Jan 10, 2024Updated 2 years ago
- Software to compute reproducibility and quality scores for Hi-C data☆52Apr 12, 2019Updated 7 years ago
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆94Jan 28, 2025Updated last year
- R package to evaluate the reproducibility of Hi-C data☆28Jun 23, 2023Updated 3 years ago
- A cool place to store your Hi-C☆243Updated this week
- A cross-platform method for chromatin contact normalization☆16Dec 29, 2025Updated 8 months 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.
- “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau☆190Jul 13, 2020Updated 6 years ago
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆44Jan 31, 2024Updated 2 years ago
- Fast, flexible and extensible genome browser.☆341Jun 17, 2026Updated 2 months ago
- Python reimplementation of hicrep with compatibility for sparse matrices☆21Dec 18, 2022Updated 3 years ago
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆68Jun 7, 2019Updated 7 years ago
- A pipeline for identifying conserved topologically associating domain boundaries among multiple species.☆17Jun 17, 2025Updated last year
- Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.☆39Apr 20, 2026Updated 4 months ago