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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 http://f1000.com/posters/browse/summary/1094053

https://github.com/deeptools/deepTools
doi: 10.1093/nar/gku365
Wikipage: https://github.com/deeptools/deepTools/wiki

Repository-Maintainer: Björn Grüning

https://github.com/deeptools/deepTools
Type: unrestricted
Revision: 5:5c5c6aff3732
This revision can be installed: True
Times cloned / installed: 4079
Dependencies of this repository

Repository package_ucsc_tools_312 revision 2d6bafd63401 owned by iuc
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
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Repository package_python_2_7_10 revision bd7165ea6526 owned by iuc (prior install required)
Repository package_atlas_3_10 revision 98c017ec230d owned by iuc (prior install required)
Repository package_python_2_7_numpy_1_9 revision f24fc0b630fc owned by iuc (prior install required)
Repository package_python_2_7_10 revision bd7165ea6526 owned by iuc (prior install required)
Repository package_python_2_7_10 revision bd7165ea6526 owned by iuc (prior install required)
Repository package_python_2_7_numpy_1_9 revision f24fc0b630fc owned by iuc (prior install required)
Repository package_python_2_7_10 revision bd7165ea6526 owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 588666932a32 owned by iuc (prior install required)
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Name Version Type
deepTools 2.2.2 package
python 2.7.10 package

Contents of this repository

Name Description Version Minimum Galaxy Version
generates a coverage bigWig file from a given BAM file 2.2.2.0 any

extension type mimetype subclass
deeptools_compute_matrix_archive galaxy.datatypes.binary:CompressedArchive True
deeptools_coverage_matrix galaxy.datatypes.binary:CompressedArchive True

Categories
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