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

Fidel Ramírez; Devon Ryan; Björn Grüning; Vivek Bhardwaj; Fabian Kilpert; Andreas S. Richter; Steffen Heyne; Friederike Dündar · Nucleic Acids Research · 2016

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Fidel Ramírez; Devon Ryan; Björn Grüning; Vivek Bhardwaj; Fabian Kilpert; Andreas S. Richter; Steffen Heyne; Friederike Dündar

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Nucleic Acids Research

Year

2016

Language

English

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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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APA 7

Ramírez, F, Ryan, D, Grüning, B, Bhardwaj, V, Kilpert, F, Richter, A. S, Heyne, S, & Dündar, F. (2016). deepTools2: a next generation web server for deep-sequencing data analysis. https://doi.org/10.1093/nar/gkw257

MLA

Ramírez, Fidel, et al. "deepTools2: a next generation web server for deep-sequencing data analysis." 2016. https://doi.org/10.1093/nar/gkw257.

Chicago

Ramírez, Fidel, Devon Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, and Friederike Dündar. 2016. "deepTools2: a next generation web server for deep-sequencing data analysis.". https://doi.org/10.1093/nar/gkw257.

Harvard

Ramírez, F. et al. 2016, deepTools2: a next generation web server for deep-sequencing data analysis, Nucleic Acids Research, available at: https://doi.org/10.1093/nar/gkw257 [Accessed 5 Aug. 2026].

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

Author / contributors: Fidel Ramírez; Devon Ryan; Björn Grüning; Vivek Bhardwaj; Fabian Kilpert; Andreas S. Richter; Steffen Heyne; Friederike Dündar

Publisher: Nucleic Acids Research

Publication year: 2016

Language: English

Subjects

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Visualization; Suite; Web server; Workflow; Computer science; Set (abstract data type); OS X; Web service; Cluster analysis; Web application; World Wide Web; The Internet