Mercurial > repos > ethevenot > batchcorrection

comparison README.md @ 0:b74d1d533dea draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
author ethevenot
date Thu, 04 Aug 2016 11:40:35 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:b74d1d533dea
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 ***