Galaxy HiCExplorer

https://hicexplorer.usegalaxy.eu/

Methods

linear single view single scale single focus contiguous no abstraction linear orthogonal arrangement within interconnection segment sparse type segment contiguous type point sparse type point contiguous type

Tool

Access Format: web application Supported Files: fasta License: MIT

Paper

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.

Wolff J, Bhardwaj V, Nothjunge S, Richard G, Renschler G, Gilsbach R, et al. Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. Nucleic Acids Res. academic.oup.com; 2018;46: W11–W16.

Cited by: 7

Abstract

Galaxy HiCExplorer is a web server that facilitates the study of the 3D conformation of chromatin by allowing Hi-C data processing, analysis and visualization. With the Galaxy HiCExplorer web server, users with little bioinformatic background can perform every step of the analysis in one workflow: mapping of the raw sequence data, creation of Hi-C contact matrices, quality assessment, correction of contact matrices and identification of topological associated domains (TADs) and A/B compartments. Users can create publication ready plots of the contact matrix, A/B compartments, and TADs on a selected genomic locus, along with additional information like gene tracks or ChIP-seq signals. Galaxy HiCExplorer is freely usable at: https://hicexplorer.usegalaxy.eu and is available as a Docker container: https://github.com/deeptools/docker-galaxy-hicexplorer.