Mercurial > repos > ethevenot > batchcorrection
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planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
author | ethevenot |
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date | Thu, 04 Aug 2016 11:40:35 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Thu Aug 04 11:40:35 2016 -0400 @@ -0,0 +1,66 @@ +## Signal drift and batch-effect correction +#### A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project + +Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/batchcorrection.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/batchcorrection). + +### Description + +**Version:** 2.0.6 +**Date:** 2016-08-02 +**Author:** Jean-François Martin (INRA, AXIOM), Mélanie Pétéra (INRA, PFEM), Marion Landi (INRA, PFEM), Franck Giacomoni (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST) +**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) +**Citation:** +**Licence:** CeCILL +**Reference history:** [W4M00001b_sacurine-complete](http://galaxy.workflow4metabolomics.org/history/list_published) +**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) + +### Installation + +* Configuration files: + + **batch_correction.xml** (for the "Batch Correction" module) + + **determine_bc.xml** (for the "Determine Batch Correction" module) +* Image files: + + **static/images/batch_correction.png** + + **static/images/determine_batch_correction.png** + + **static/images/pdf_plotsituation.png** + + **static/images/Vdk_pdf1.png** + + **static/images/Vdk_pdf2.png** +* Wrapper files: + + **batch_correction_wrapper.R** + + **batch_correction_all_loess_wrapper.R** +* Script files: + + **Normalisation_QCpool.r** + + **miniTools.R** + + **RcheckLibrary.R** + + **batch_correction_all_loess_script.R** +* R packages + + **batch** from CRAN +> install.packages("batch", dep=TRUE) + + **ade4** from CRAN +> install.packages("ade4", dep=TRUE) + + **pcaMethods** from Bioconductor +> source("http://www.bioconductor.org/biocLite.R") +> biocLite("pcaMethods") + + **ropls** from Bioconductor +> source("http://www.bioconductor.org/biocLite.R") +> biocLite("ropls") + +### Tests + +The code in the batch_correction_wrapper can be tested by running the **runit/batchcorrection_runtests.R** in R + +### News + +##### CHANGES IN VERSION 2.0.6 + +INTERNAL MODIFICATIONS + + o Additional running and installation tests added with planemo, conda, and travis + +##### CHANGES IN VERSION 2.0.4 + +INTERNAL MODIFICATION + + o 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) + +*** \ No newline at end of file