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Repository deeptools_bam_coverage
Owner: bgruening
Synopsis: Wrapper for the deepTools: bamCoverage
deepTools address the challenge of visualizing the large amounts of data that
are now routinely generated from sequencing centers in a meaningful way. To do so,
deepTools contain useful routines to process the mapped reads data through removal of
duplicates and different filtering options to create coverage files in standard
bedGraph and bigWig file formats. deepTools allow the creation of normalized
coverage files or the comparison between two files (for example, treatment and control).

Finally, using such normalized and standardized files, multiple visualizations can be
created to identify enrichments with functional annotations of the genome.
For a gallery of images that can be produced and a description of the tools see
doi: 10.1093/nar/gku365

Repository-Maintainer: Björn Grüning
Type: unrestricted
Revision: 26:bb1e4f63e0e6
This revision can be installed: True
Times cloned / installed: 4939

Repository README files - may contain important installation or license information

======================== Galaxy deeptools wrapper ======================== deepTools are user-friendly tools for the normalization and visualization of deep-sequencing data. They address the challenge of visualizing the large amounts of data that are now routinely generated from sequencing centers in a meaningful way. To do so, deepTools contain useful routines to process the mapped reads data through removal of duplicates and different filtering options to create coverage files in standard bedGraph and bigWig file formats. deepTools allow the creation of normalized coverage files or the comparison between two files (for example, treatment and control). Finally, using such normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome. For a gallery of images that can be produced and a description of the tools see our poster_. .. _poster: deeptools is developed under here: For support or questions please post to `Biostars `__. For bug reports and feature requests please open an issue ``__. ============ Installation ============ Requirements: python-2.7 Galaxy should be able to automatically install all other dependencies, such as numpy or scipy. For the best performance we recommend to install blas/lapack/atlas in your environment before installing deepTools from the Tool Shed. ======== Citation ======== deeptools are currently under review. In the meantime please refere to ======= History ======= * v1.0: Initial public release * v1.5.8.2: Include new citation tag, update version to and change wrapper version Licence (MIT) ============= Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Dependencies of this repository

Repository data_manager_twobit_builder revision 625fd9476402 owned by devteam

Contents of this repository

Name Description Version Minimum Galaxy Version
generates a coverage bigWig file from a given BAM or CRAM file 16.01

ChIP-seq - Tools for analyzing and manipulating ChIP-seq data.
Convert Formats - Tools for converting data formats
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis
Visualization - Tools for visualizing data