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

Wolff, Joachim; Bhardwaj, Vivek; Nothjunge, Stephan; Richard, Gautier; Renschler, Gina; Gilsbach, Ralf; Manke, Thomas; Backofen, Rolf; Ramirez, Fidel; Grüning, Björn A.

doi:10.1093/nar/gkaa220

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

MPS-Authors

Bhardwaj, Vivek
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Manke, Thomas
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Ramirez, Fidel
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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https://academic.oup.com/nar/article/48/W1/W177/5821269
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Citation

Wolff, J., Bhardwaj, V., Nothjunge, S., Richard, G., Renschler, G., Gilsbach, R., et al. (2020). Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. Nucleic Acids Research (London), 48, W117-W184. doi: 10.1093/nar/gkaa220.

Cite as: https://hdl.handle.net/21.11116/0000-0003-6E23-B

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.