The tools for your .cool's
☆164Mar 19, 2026Updated 2 months ago
Alternatives and similar repositories for cooltools
Users that are interested in cooltools are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A cool place to store your Hi-C☆237Apr 27, 2026Updated 3 weeks ago
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated last year
- Extract 3D contacts (.pairs) from sequencing alignments☆132Feb 3, 2026Updated 3 months ago
- A modular Hi-C mapping pipeline☆102Dec 5, 2024Updated last year
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆81Oct 31, 2024Updated last year
- 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.
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆71Dec 16, 2022Updated 3 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
- FAN-C: Framework for the ANalysis of C-like data☆121Mar 13, 2024Updated 2 years ago
- A collection of tools for Hi-C data analysis☆641Updated this week
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆78Jul 22, 2025Updated 9 months ago
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆272Jul 17, 2025Updated 10 months ago
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆481Aug 31, 2025Updated 8 months ago
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆67Jun 7, 2019Updated 6 years ago
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆92Jan 28, 2025Updated last year
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆82Jan 24, 2025Updated last year
- Genome-wide contact analysis using sklearn☆74Mar 23, 2024Updated 2 years ago
- multiway chromatin interaction, 3D genome, single-nucleus, hypergraph representation learning☆31Jul 20, 2022Updated 3 years ago
- SIP: Significant Interaction Peak caller☆17Apr 24, 2025Updated last year
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 4 months ago
- Genomic interval operations on Pandas DataFrames☆191May 4, 2026Updated 2 weeks ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph☆92Oct 29, 2025Updated 6 months ago
- Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…☆94Aug 29, 2022Updated 3 years ago
- Python bindings to and Jupyter Notebook+Lab integration for the HiGlass viewer☆65May 12, 2026Updated last week
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Package for analysis and characterization of differential TADs☆27Apr 25, 2022Updated 4 years ago
- 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 last month
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 years ago
- Micro-C QC and data analysis☆16Aug 1, 2023Updated 2 years ago
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 3 years ago
- nuclear compartments, subcompartments, nuclear organization, Hi-C, autoencoder☆28Jul 5, 2024Updated last year
- Cooler demo using a Jupyter notebook Binder☆18Sep 24, 2020Updated 5 years ago
- Blazing fast toolkit to work with .hic and .cool files☆44May 11, 2026Updated last week
- Python bindings to UCSC BigWig and BigBed library☆36Apr 6, 2026Updated last month
- 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.
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆436Mar 28, 2024Updated 2 years ago
- Jupyter notebook based genomic data visualization toolkit.☆257Dec 4, 2025Updated 5 months ago
- Fast alignment and preprocessing of chromatin profiles☆219Mar 20, 2026Updated last month
- Chromosome polymer simulations and in silico capture experiments☆58Feb 18, 2026Updated 3 months ago
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 2 years ago
- Visualization and analysis software for Hi-C data -☆295Aug 6, 2024Updated last year
- Extract data quickly from Juicebox via straw☆70Apr 6, 2025Updated last year