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  deepTools2: a next generation web server for deep-sequencing data analysis

Ramirez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., et al. (2016). deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research (London), 44, W160-W165. doi:10.1093/nar/gkw257.

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Item Permalink: https://hdl.handle.net/11858/00-001M-0000-002C-B130-8 Version Permalink: https://hdl.handle.net/21.11116/0000-0008-A588-4
Genre: Journal Article

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https://academic.oup.com/nar/article/44/W1/W160/2499308 (Publisher version)
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 Creators:
Ramirez, Fidel1, Author
Ryan, Devon P.1, Author
Grüning, Björn2, Author
Bhardwaj, Vivek1, 3, Author
Kilpert, Fabian1, Author
Richter, Andreas S.1, Author
Heyne, Steffen1, Author
Dündar, Friederike4, Author
Mnake, Thomas1, Author
Affiliations:
1Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, 79108 Freiburg, DE, ou_2243640              
2University of Freiburg, Department of Computer Science, Freiburg, Germany, ou_persistent22              
3Faculty of Biology, University of Freiburg, Freiburg, Germany, ou_persistent22              
4Weill Cornell Medical College, Applied Bioinformatics Core, Department of Physiology and Biophysics, New York, USA, ou_persistent22              

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 Abstract: We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available.

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Language(s): eng - English
 Dates: 2016-07-08
 Publication Status: Issued
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1093/nar/gkw257
 Degree: -

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Title: Nucleic Acids Research (London)
  Other : Nucleic Acids Res
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 44 Sequence Number: - Start / End Page: W160 - W165 Identifier: ISSN: 0305-1048
CoNE: https://pure.mpg.de/cone/journals/resource/110992357379342