Mercurial > repos > ethevenot > biosigner
annotate README.md @ 1:4ff502a46189 draft
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit 8f8ca9d7be625518f878eae833c8d55eb64c7761
author | ethevenot |
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date | Sat, 30 Jul 2016 12:21:07 -0400 |
parents | 48e4be935243 |
children | b2414be87d4b |
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48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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1 Discovery of significant signatures from omics data |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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2 =================================================== |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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3 |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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5 |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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6 Status: [](https://travis-ci.org/workflow4metabolomics/biosigner). |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
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7 |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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8 ## Description |
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planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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9 |
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4ff502a46189
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit 8f8ca9d7be625518f878eae833c8d55eb64c7761
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10 **Version:** 2.2.4 |
4ff502a46189
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit 8f8ca9d7be625518f878eae833c8d55eb64c7761
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11 **Date:** 2016-07-30 |
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48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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12 **Author:** Philippe Rinaudo and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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14 **Citation:** Rinaudo P., Boudah S., Junot C. and Thevenot E.A. (2015). biosigner: A new method for the discovery of restricted and stable molecular signatures from omics data. *Frontiers in Molecular Biosciences*, in review. |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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15 **Licence:** CeCILL |
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planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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16 **Reference history:** [W4M00003_diaplasma](http://galaxy.workflow4metabolomics.org/history/list_published) |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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17 **Funding:** Agence Nationale de la Recherche ([MetaboHUB](http://www.metabohub.fr/index.php?lang=en&Itemid=473) national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant) |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
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18 |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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19 ## Installation |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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20 |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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21 * Configuration file: `biosigner_config.xml`. |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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22 * Image files: |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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23 + `static/images/biosigner_workflowPositionImage.png`. |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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24 + `static/images/biosigner_workingExampleImage.png`. |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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25 * Wrapper file: `biosigner_wrapper.R`. |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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26 * R packages |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
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27 + **batch** from CRAN: `install.packages("batch", dep=TRUE)`. |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
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28 + **biosigner** from Bioconductor (which itself depends on **ropls** from Bioconductor and **e1071** and **randomForest** from CRAN): `source("http://www.bioconductor.org/biocLite.R") ; biocLite("biosigner")`. |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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29 |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
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30 ## Tests |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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31 |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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32 The code in the wrapper can be tested by running the `tests/biosigner_tests.R` in R |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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33 |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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34 ## News |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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35 |
1
4ff502a46189
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit 8f8ca9d7be625518f878eae833c8d55eb64c7761
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36 ## CHANGES IN VERSION 2.2.4 |
4ff502a46189
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit 8f8ca9d7be625518f878eae833c8d55eb64c7761
ethevenot
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37 |
4ff502a46189
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit 8f8ca9d7be625518f878eae833c8d55eb64c7761
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38 * Internal updates for planemo and travis validation |
4ff502a46189
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit 8f8ca9d7be625518f878eae833c8d55eb64c7761
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39 |
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48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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40 ## CHANGES IN VERSION 2.2.2 |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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41 |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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42 * Internal updates to biosigner package versions of 1.0.0 and above, and ropls versions of 1.4.0 and above (i.e. using S4 methods instead of S3) |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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43 |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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44 ## CHANGES IN VERSION 2.2.1 |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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45 |
48e4be935243
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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46 * Creation of the tool: with S3 versions of biosigner (< 1.0.0) and ropls (< 1.4.0) |