Mercurial > repos > ethevenot > batchcorrection
comparison README.md @ 0:b74d1d533dea draft default tip
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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1 ## Signal drift and batch-effect correction | |
2 #### A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project | |
3 | |
4 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/batchcorrection.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/batchcorrection). | |
5 | |
6 ### Description | |
7 | |
8 **Version:** 2.0.6 | |
9 **Date:** 2016-08-02 | |
10 **Author:** Jean-François Martin (INRA, AXIOM), Mélanie Pétéra (INRA, PFEM), Marion Landi (INRA, PFEM), Franck Giacomoni (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST) | |
11 **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) | |
12 **Citation:** | |
13 **Licence:** CeCILL | |
14 **Reference history:** [W4M00001b_sacurine-complete](http://galaxy.workflow4metabolomics.org/history/list_published) | |
15 **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) | |
16 | |
17 ### Installation | |
18 | |
19 * Configuration files: | |
20 + **batch_correction.xml** (for the "Batch Correction" module) | |
21 + **determine_bc.xml** (for the "Determine Batch Correction" module) | |
22 * Image files: | |
23 + **static/images/batch_correction.png** | |
24 + **static/images/determine_batch_correction.png** | |
25 + **static/images/pdf_plotsituation.png** | |
26 + **static/images/Vdk_pdf1.png** | |
27 + **static/images/Vdk_pdf2.png** | |
28 * Wrapper files: | |
29 + **batch_correction_wrapper.R** | |
30 + **batch_correction_all_loess_wrapper.R** | |
31 * Script files: | |
32 + **Normalisation_QCpool.r** | |
33 + **miniTools.R** | |
34 + **RcheckLibrary.R** | |
35 + **batch_correction_all_loess_script.R** | |
36 * R packages | |
37 + **batch** from CRAN | |
38 > install.packages("batch", dep=TRUE) | |
39 + **ade4** from CRAN | |
40 > install.packages("ade4", dep=TRUE) | |
41 + **pcaMethods** from Bioconductor | |
42 > source("http://www.bioconductor.org/biocLite.R") | |
43 > biocLite("pcaMethods") | |
44 + **ropls** from Bioconductor | |
45 > source("http://www.bioconductor.org/biocLite.R") | |
46 > biocLite("ropls") | |
47 | |
48 ### Tests | |
49 | |
50 The code in the batch_correction_wrapper can be tested by running the **runit/batchcorrection_runtests.R** in R | |
51 | |
52 ### News | |
53 | |
54 ##### CHANGES IN VERSION 2.0.6 | |
55 | |
56 INTERNAL MODIFICATIONS | |
57 | |
58 o Additional running and installation tests added with planemo, conda, and travis | |
59 | |
60 ##### CHANGES IN VERSION 2.0.4 | |
61 | |
62 INTERNAL MODIFICATION | |
63 | |
64 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) | |
65 | |
66 *** |