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planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
author ethevenot
date Wed, 27 Jul 2016 11:40:20 -0400
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1 Discovery of significant signatures from omics data
2 ===================================================
3
4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project
5
6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/biosigner.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/biosigner).
7
8 ## Description
9
10 **Version:** 2.2.2
11 **Date:** 2016-05-21
12 **Author:** Philippe Rinaudo and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
14 **Citation:** Rinaudo P., Boudah S., Junot C. and Thevenot E.A. (2015). biosigner: A new method for the discovery of restricted and stable molecular signatures from omics data. *Frontiers in Molecular Biosciences*, in review.
15 **Licence:** CeCILL
16 **Reference history:** [W4M00003_diaplasma](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 file: `biosigner_config.xml`.
22 * Image files:
23 + `static/images/biosigner_workflowPositionImage.png`.
24 + `static/images/biosigner_workingExampleImage.png`.
25 * Wrapper file: `biosigner_wrapper.R`.
26 * R packages
27 + **batch** from CRAN: `install.packages("batch", dep=TRUE)`.
28 + **biosigner** from Bioconductor (which itself depends on **ropls** from Bioconductor and **e1071** and **randomForest** from CRAN): `source("http://www.bioconductor.org/biocLite.R") ; biocLite("biosigner")`.
29
30 ## Tests
31
32 The code in the wrapper can be tested by running the `tests/biosigner_tests.R` in R
33
34 ## News
35
36 ## CHANGES IN VERSION 2.2.2
37
38 * Internal updates to biosigner package versions of 1.0.0 and above, and ropls versions of 1.4.0 and above (i.e. using S4 methods instead of S3)
39
40 ## CHANGES IN VERSION 2.2.1
41
42 * Creation of the tool: with S3 versions of biosigner (< 1.0.0) and ropls (< 1.4.0)