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planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
author melpetera
date Tue, 09 Aug 2016 06:47:41 -0400
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1 Signal drift and batch-effect correction
2 ========================================
3
4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
5
6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/batchcorrection.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/batchcorrection).
7
8 ### Description
9
10 **Version:** 2.0.6
11 **Date:** 2016-08-02
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)
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)
14 **Citation:**
15 **Licence:** CeCILL
16 **Reference history:** [W4M00001b_sacurine-complete](http://galaxy.workflow4metabolomics.org/history/list_published)
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)
18
19 ### Installation
20
21 * Configuration files:
22 + `batch_correction.xml` (for the "Batch Correction" module)
23 + `determine_bc.xml` (for the "Determine Batch Correction" module)
24 * Image files:
25 + `static/images/batch_correction.png`
26 + `static/images/determine_batch_correction.png`
27 + `static/images/pdf_plotsituation.png`
28 + `static/images/Vdk_pdf1.png`
29 + `static/images/Vdk_pdf2.png`
30 * Wrapper files:
31 + `batch_correction_wrapper.R`
32 + `batch_correction_all_loess_wrapper.R`
33 * Script files:
34 + `Normalisation_QCpool.r`
35 + `batch_correction_all_loess_script.R`
36 * R packages
37 + **batch** from CRAN
38
39 ```r
40 install.packages("batch", dep=TRUE)
41 ```
42
43 + **ade4** from CRAN
44
45 ```r
46 install.packages("ade4", dep=TRUE)
47 ```
48
49 + **pcaMethods** from Bioconductor
50
51 ```r
52 source("http://www.bioconductor.org/biocLite.R")
53 biocLite("pcaMethods")
54 ```
55
56 + **ropls** from Bioconductor
57
58 ```r
59 source("http://www.bioconductor.org/biocLite.R")
60 biocLite("ropls")
61 ```
62
63 ### Tests
64
65 The code in the batch_correction_wrapper can be tested by running the `runit/batchcorrection_runtests.R` R file
66
67 You will need to install **RUnit** package in order to make it run:
68 ```r
69 install.packages('RUnit', dependencies = TRUE)
70 ```
71
72 ### Working example
73
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)
75
76 ### News
77
78 ##### CHANGES IN VERSION 2.0.6
79
80 INTERNAL MODIFICATIONS
81
82 * Additional running and installation tests added with planemo, conda, and travis
83
84 ##### CHANGES IN VERSION 2.0.4
85
86 INTERNAL MODIFICATION
87
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)