Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
| Autor: | Joachim Wolff, Gautier Richard, Gina Renschler, Vivek Bhardwaj, Thomas Manke, Stephan Nothjunge, Fidel Ramírez, Ralf Gilsbach, Björn Grüning, Rolf Backofen |
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| Přispěvatelé: | University of Freiburg [Freiburg], Max Planck Society, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, SFB 992/2 2016, Deutsche Forschungsgemeinschaft, 01KU1216G, Bundesministerium für Bildung und Forschung, 747/2-1, DFG project, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro) |
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
Data Analysis
0301 basic medicine Web server Bioinformatics Biology computer.software_genre USable analyse de génome 03 medical and health sciences Software séquençage Genetics site web bioinformatique Internet Genome Information retrieval business.industry Computational Biology High-Throughput Nucleotide Sequencing Genomics Chromatin Visualization Identification (information) 030104 developmental biology Workflow cartographie du génome Web Server Issue Container (abstract data type) Bio-informatique The Internet [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] business computer |
| Zdroj: | Nucleic Acids Research Nucleic Acids Research, 2018, 46 (W1), pp.W11-W16. ⟨10.1093/nar/gky504⟩ Nucleic Acids Research (London) Nucleic Acids Research, Oxford University Press, 2018, 46 (W1), pp.W11-W16. ⟨10.1093/nar/gky504⟩ Nucleic Acids Research W1 (46), W11-W16. (2018) |
| ISSN: | 0305-1048 1362-4962 |
| DOI: | 10.1093/nar/gky504⟩ |
| Popis: | International audience; 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. |
| Databáze: | OpenAIRE |
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