Mercurial > repos > bgruening > deeptools
diff readme.rst @ 26:2ad3b027dfcd draft
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author | bgruening |
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date | Thu, 06 Feb 2014 06:40:05 -0500 |
parents | d2898b81b912 |
children | f7712a057440 |
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--- a/readme.rst Tue Feb 04 13:45:17 2014 -0500 +++ b/readme.rst Thu Feb 06 06:40:05 2014 -0500 @@ -1,41 +1,61 @@ -This package contains a collection of Galaxy workflows utilising deepTools. +======================== +Galaxy deeptools wrapper +======================== -See http://www.galaxyproject.org for information about the Galaxy Project. +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: http://f1000.com/posters/browse/summary/1094053 + +deeptools is developed under here: + + https://github.com/fidelram/deepTools + +For support, questions, or feature requests contact: deeptools@googlegroups.com -Sample Data -=========== - -Sample data can be obtained from http://deeptools.ie-freiburg.mpg.de/library or you -can use aligned reads in BAM or SAM format. - - - +======== Citation ======== -If you use this workflow directly, or a derivative of it, or the associated -deepTools wrappers for Galaxy, in work leading to a scientific publication, -please cite: +deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools. + -{publication under review} +======= +History +======= + +- v1.0: Initial public release -Availability -============ +Licence (MIT) +============= -This workflow is available on the main Galaxy Tool Shed: - -http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows - -Development is being done on github: +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: -https://github.com/fidelram/deepTools - +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. -Dependencies -============ - -These dependencies should be resolved automatically via the Galaxy Tool Shed: - -* http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools +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.