A visual exploration and hypothesis testing tool for 3D genomics
☆13Apr 12, 2024Updated last year
Alternatives and similar repositories for hicognition
Users that are interested in hicognition 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 library to analyse the structure of 1d loops and simulate loop extrusion by loop extruding factors.☆11Feb 10, 2025Updated last year
- Red-C data processing☆15Apr 18, 2023Updated 2 years ago
- pyranges/bioframe for polars☆18Jul 20, 2023Updated 2 years ago
- Slides and demos from our SciPyConf 2019 talk☆13Sep 28, 2021Updated 4 years ago
- Architectural stripe detection from 3D genome conformation data☆18Sep 15, 2025Updated 6 months ago
- Methods for summarizing and visualizing multi-biosample functional genomic annotations☆47Mar 26, 2025Updated 11 months ago
- Chromosome polymer simulations and in silico capture experiments☆56Feb 18, 2026Updated last month
- Python bindings to UCSC BigWig and BigBed library☆36Mar 13, 2026Updated last week
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 2 years ago
- Plotting average TAD heatmap for Hi-C data (give TAD segmentation and cool/hiclib interactions map).☆10Jun 5, 2021Updated 4 years ago
- Rusty juv☆13Nov 7, 2024Updated last year
- A command-line tool for reading SAM/BAM files and converted them directly to bigwig files.☆21Jan 3, 2026Updated 2 months ago
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆41Jan 31, 2024Updated 2 years ago
- A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.☆14Mar 9, 2023Updated 3 years ago
- A modular Hi-C mapping pipeline☆101Dec 5, 2024Updated last year
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆77Jul 22, 2025Updated 8 months ago
- Prototype your Jupyter Widget in the browser with anywidget and JupyterLite 💡☆17Apr 7, 2025Updated 11 months ago
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆81Oct 31, 2024Updated last year
- Genomic interval operations on Pandas DataFrames☆191Mar 2, 2026Updated 3 weeks ago
- Single-cell Hi-C data analysis toolbox☆27Aug 13, 2021Updated 4 years ago
- A toolkit for analyzing architectural stripes☆20Dec 1, 2024Updated last year
- Code and data used to create the JASPAR UCSC Genome Browser tracks data hub☆18Dec 11, 2025Updated 3 months ago
- Pore-C support☆54Feb 22, 2023Updated 3 years ago
- Scripts to create cartoons of 3D genomes☆12Feb 27, 2024Updated 2 years ago
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Dec 16, 2022Updated 3 years ago
- cudami is a Digital Asset Management System for management and editing of cultural objects.☆21Updated this week
- Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.☆39Mar 17, 2026Updated last week
- Extract 3D contacts (.pairs) from sequencing alignments☆128Feb 3, 2026Updated last month
- Python reimplementation of hicrep with compatibility for sparse matrices☆19Dec 18, 2022Updated 3 years ago
- PHi-C: deciphering Hi-C data into polymer dynamics☆11Aug 12, 2020Updated 5 years ago
- A modified Ziggurat Algorithm for efficiently generating exponentially- and normally-distributed PseudoRandom Numbers (PRNs).☆13May 21, 2025Updated 10 months ago
- a minimal, scriptable genome browser for python☆53Dec 20, 2024Updated last year
- Terminal-based multiple sequence alignment (MSA) viewer designed for remote and HPC bioinformatics workflows.☆27Feb 3, 2026Updated last month
- FreeHi-C pipeline for high fidelity Hi-C data simulation.☆12Jul 13, 2021Updated 4 years ago
- ☆10Apr 24, 2024Updated last year
- Blacklight instance over Ex Libris Alma☆13Dec 14, 2022Updated 3 years ago
- ☆22May 26, 2020Updated 5 years ago
- A declarative interactive genomics visualization library for Python.☆243Nov 24, 2025Updated 4 months ago
- Enhanced Chromatin Occupancy (EChO)☆13Jan 8, 2020Updated 6 years ago