Chromosight: A computer vision program for pattern detection in chromosome contact maps
Cyril Matthey-DoretiD, Lyam BaudryiD, Axel Breuer, Rémi MontagneiD, Nadège GuiglielmoniiD, Vittore F. ScolariiD, Étienne Jean, Arnaud Campeas, Philippe Henri Chanut, Edgar OrioliD, Adrien Méot, Laurent Politis, A. VigourouxiD, Pierrick MoreauiD, Romain KoszuliD, Axel CournaciD
Abstract
Chromosomes of all species studied so far display a variety of higher order organizational features such as domains or loops often associated to biological functions and visible on Hi-C contact maps. We developed Chromosight, an algorithm inspired from computer vision that can detect patterns in Hi-C maps. Chromosight has greater sensitivity than existing methods, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Code and documentation: https://github.com/koszullab/chromosight
02 /Specification & Classification
Click any tag to browse matching papers- Citations
- 132
- FWCI
- 3.73
- Field percentile
- top 5%
- Assay
- Approach
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Boost-HiC : Computational enhancement of long-range contacts in chromosomal contact maps
Léopold Carron, Jean Baptiste Morlot, … Julien Mozziconacci·BioinformaticsPeer-reviewed·Dec 28, 2018
- Hi-Cpipe: a pipeline for high-throughput chromosome capture
Giancarlo Castellano, François Le Dily, … Guglielmo Roma·bioRxiv·Jun 19, 2015
- Revisiting the Use of Structural Similarity Index in Hi-C
Hanjun Lee, Bruce Blumberg, … Toshi Shioda·Nature GeneticsPeer-reviewed·Dec 1, 2023
- Mustache: Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
Abbas Roayaei Ardakany, Halil Tuvan Gezer, … Ferhat Ay·Genome biologyPeer-reviewed·Sep 30, 2020
- Loop detection using Hi-C data with HiCExplorer
Joachim Wolff, Rolf Backofen, Björn Andreas Grüning·GigaSciencePeer-reviewed·Jan 1, 2022
- StripePy: fast and robust characterization of architectural stripes
Andrea Raffo, Roberto Rossini, Jonas Paulsen·BioinformaticsPeer-reviewed·Jun 1, 2025