Chromosome polymer simulations and in silico capture experiments
☆56Feb 18, 2026Updated last month
Alternatives and similar repositories for polychrom
Users that are interested in polychrom 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
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆81Oct 31, 2024Updated last year
- Python bindings to UCSC BigWig and BigBed library☆36Mar 13, 2026Updated last week
- snakemake pipeline for Hi-C post-processing☆22Jun 27, 2024Updated last year
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Dec 16, 2022Updated 3 years ago
- A visual exploration and hypothesis testing tool for 3D genomics☆13Apr 12, 2024Updated last year
- A cool place to store your Hi-C☆231Mar 16, 2026Updated last week
- The tools for your .cool's☆161Jul 7, 2025Updated 8 months ago
- A modular Hi-C mapping pipeline☆101Dec 5, 2024Updated last year
- Plotting average TAD heatmap for Hi-C data (give TAD segmentation and cool/hiclib interactions map).☆10Jun 5, 2021Updated 4 years ago
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 years ago
- A toolkit for analyzing architectural stripes☆20Dec 1, 2024Updated last year
- Extract 3D contacts (.pairs) from sequencing alignments☆126Feb 3, 2026Updated last month
- Red-C data processing☆15Apr 18, 2023Updated 2 years 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
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆80Jan 24, 2025Updated last year
- High-performance stochastic modeling of DNA loop extrusion interactions☆18Dec 22, 2025Updated 3 months ago
- A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.☆14Mar 9, 2023Updated 3 years ago
- A collection of tools for Hi-C data analysis☆633Mar 15, 2026Updated last week
- Architectural stripe detection from 3D genome conformation data☆18Sep 15, 2025Updated 6 months ago
- Blazing fast toolkit to work with .hic and .cool files☆42Updated this week
- pyranges/bioframe for polars☆18Jul 20, 2023Updated 2 years ago
- Genome-wide contact analysis using sklearn☆74Mar 23, 2024Updated 2 years ago
- Genomic interval operations on Pandas DataFrames☆191Mar 2, 2026Updated 3 weeks ago
- Chromatin domains bursting with flavor☆12Dec 29, 2019Updated 6 years ago
- Python bindings for hictk: read and write .cool and .hic files directly from Python☆16Updated this week
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆77Jul 22, 2025Updated 8 months ago
- HiCorr: a Hi-C data bias-correction pipeline☆30Apr 1, 2025Updated 11 months ago
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 2 years ago
- Lightweight converter between hic and cool contact matrices.☆75Jul 15, 2024Updated last year
- ☆13Jul 21, 2021Updated 4 years ago
- Python reimplementation of hicrep with compatibility for sparse matrices☆19Dec 18, 2022Updated 3 years ago
- SIP: Significant Interaction Peak caller☆16Apr 24, 2025Updated 10 months ago
- Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.☆39Updated this week
- Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the…☆23Jun 4, 2023Updated 2 years ago
- A GAN-based method for Enhancing Hi-C data☆33Dec 17, 2020Updated 5 years ago
- R functions for very fast eigenvector calculation☆11Jan 18, 2023Updated 3 years ago
- R package to evaluate the reproducibility of Hi-C data☆27Jun 23, 2023Updated 2 years ago
- ☆11Apr 4, 2023Updated 2 years ago