Supported Applications
deepTools
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Description
a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.
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Installation
Use the following command to install this title with the CLI client:$ sbgrid-cli install deeptools
Available operating systems: Linux 64, OS X INTEL -
Primary Citation*
F. Ramírez, D. P. Ryan, B. Grüning, V. Bhardwaj, F. Kilpert, A. S. Richter, S. Heyne, F. Dündar, and T. Manke. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research. 44(1): W160-W165.
(Note: Web Server issue)-
*Full citation information available through
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Keywords
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Default Versions
Linux 64:  3.5.1 (485.1 MB)
OS X INTEL:  3.5.1 (439.4 MB) -
Other Versions
Linux 64:
3.3.1 (1.1 GB) -
OS X INTEL:
3.3.1 (412.2 MB)
Developers
Thomas Manke, Devon Ryan, Fidel Ramírez