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  deep Tools: a flexible platform for exploring deep-sequencing data

Ramírez, F., Dündar, F., Diehl, S., Grüning, B. A., & Manke, T. (2014). deep Tools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Research, 42, W187-W191.

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 Creators:
Ramírez, Fidel1, Author
Dündar, Friederike2, Author              
Diehl, Sarah1, Author
Grüning, Björn A., Author
Manke, Thomas3, Author              
Affiliations:
1Max Planck Society, ou_persistent13              
2Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, ou_2243643              
3Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, ou_2243644              

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 Abstract: We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg.de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy.

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Language(s): eng - English
 Dates: 2014
 Publication Status: Published in print
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 Rev. Type: Peer
 Identifiers: eDoc: 701941
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Title: Nucleic Acids Research
Source Genre: Journal
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Pages: - Volume / Issue: 42 Sequence Number: - Start / End Page: W187 - W191 Identifier: -