Mercurial > repos > bgruening > deeptools_bigwig_compare
annotate readme.rst @ 16:c4d74248ce60 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4abb1e731efdaa32fadb32c9e23883f7c17fb85c
author | bgruening |
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date | Mon, 05 Feb 2018 11:39:57 -0500 |
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1 ======================== |
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2 Galaxy deeptools wrapper |
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3 ======================== |
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4 |
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5 deepTools are user-friendly tools for the normalization and visualization of |
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6 deep-sequencing data. |
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7 They address the challenge of visualizing the large amounts of data that are now |
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8 routinely generated from sequencing centers in a meaningful way. |
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9 To do so, deepTools contain useful routines to process the mapped reads data |
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10 through removal of duplicates and different filtering options to create coverage |
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11 files in standard bedGraph and bigWig file formats. deepTools allow the creation |
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12 of normalized coverage files or the comparison between two files |
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13 (for example, treatment and control). Finally, using such normalized and |
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14 standardized files, multiple visualizations can be created to identify |
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15 enrichments with functional annotations of the genome. |
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16 For a gallery of images that can be produced and a description |
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17 of the tools see our poster_. |
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18 |
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19 .. _poster: http://f1000.com/posters/browse/summary/1094053 |
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20 |
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21 deeptools is developed under here: |
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22 |
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23 https://github.com/fidelram/deepTools |
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24 |
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25 For support, questions, or feature requests contact: deeptools@googlegroups.com |
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26 |
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27 |
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28 ============ |
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29 Installation |
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30 ============ |
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31 |
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32 Requirements: python-2.7 |
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33 |
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34 Galaxy should be able to automatically install all other dependencies, such as numpy or scipy. |
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35 |
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36 For the best performance we recommend to install blas/lapack/atlas in your environment before |
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37 installing deepTools from the Tool Shed. |
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38 |
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39 |
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40 ======== |
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41 Citation |
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42 ======== |
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43 |
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44 deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools. |
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45 |
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46 |
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47 ======= |
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48 History |
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49 ======= |
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50 |
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51 * v1.0: Initial public release |
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52 * v1.5.8.2: Include new citation tag, update version to 1.5.8.2 and change wrapper version |
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53 |
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54 |
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55 Licence (MIT) |
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56 ============= |
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57 |
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58 Permission is hereby granted, free of charge, to any person obtaining a copy |
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59 of this software and associated documentation files (the "Software"), to deal |
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60 in the Software without restriction, including without limitation the rights |
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61 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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62 copies of the Software, and to permit persons to whom the Software is |
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63 furnished to do so, subject to the following conditions: |
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64 |
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65 The above copyright notice and this permission notice shall be included in |
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66 all copies or substantial portions of the Software. |
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67 |
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68 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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69 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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70 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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71 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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72 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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73 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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74 THE SOFTWARE. |