annotate README.md @ 0:71d83d8920bf draft

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author melpetera
date Tue, 09 Aug 2016 06:47:41 -0400
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1 Signal drift and batch-effect correction
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2 ========================================
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4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
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6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/batchcorrection.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/batchcorrection).
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8 ### Description
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10 **Version:** 2.0.6
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11 **Date:** 2016-08-02
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12 **Author:** Jean-François Martin (INRA, AXIOM), Mélanie Pétéra (INRA, PFEM), Marion Landi (INRA, PFEM), Franck Giacomoni (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST)
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13 **Email:** [jean-francois.martin(at)toulouse.inra.fr](mailto:jean-francois.martin@toulouse.inra.frr), [melanie.petera(at)clermont.inra.fr](mailto:melanie.petera@clermont.inra.fr), [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
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14 **Citation:**
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15 **Licence:** CeCILL
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16 **Reference history:** [W4M00001b_sacurine-complete](http://galaxy.workflow4metabolomics.org/history/list_published)
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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)
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19 ### Installation
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21 * Configuration files:
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22 + `batch_correction.xml` (for the "Batch Correction" module)
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23 + `determine_bc.xml` (for the "Determine Batch Correction" module)
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24 * Image files:
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25 + `static/images/batch_correction.png`
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26 + `static/images/determine_batch_correction.png`
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27 + `static/images/pdf_plotsituation.png`
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28 + `static/images/Vdk_pdf1.png`
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29 + `static/images/Vdk_pdf2.png`
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30 * Wrapper files:
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31 + `batch_correction_wrapper.R`
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32 + `batch_correction_all_loess_wrapper.R`
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33 * Script files:
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34 + `Normalisation_QCpool.r`
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35 + `batch_correction_all_loess_script.R`
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36 * R packages
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37 + **batch** from CRAN
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39 ```r
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40 install.packages("batch", dep=TRUE)
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41 ```
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43 + **ade4** from CRAN
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45 ```r
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46 install.packages("ade4", dep=TRUE)
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47 ```
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49 + **pcaMethods** from Bioconductor
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51 ```r
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52 source("http://www.bioconductor.org/biocLite.R")
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53 biocLite("pcaMethods")
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54 ```
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56 + **ropls** from Bioconductor
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58 ```r
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59 source("http://www.bioconductor.org/biocLite.R")
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60 biocLite("ropls")
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61 ```
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63 ### Tests
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65 The code in the batch_correction_wrapper can be tested by running the `runit/batchcorrection_runtests.R` R file
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67 You will need to install **RUnit** package in order to make it run:
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68 ```r
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69 install.packages('RUnit', dependencies = TRUE)
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70 ```
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72 ### Working example
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74 See also the reference history **W4M00001b_sacurine-complete** shared history in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
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76 ### News
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78 ##### CHANGES IN VERSION 2.0.6
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80 INTERNAL MODIFICATIONS
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82 * Additional running and installation tests added with planemo, conda, and travis
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84 ##### CHANGES IN VERSION 2.0.4
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86 INTERNAL MODIFICATION
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88 * Modification of the 'all_loess_wrapper.R' file to handle 'ropls' package versions of 1.3.15 and above (i.e. after switching to S4 classes)