Discovery of significant signatures from omics data
===================================================

A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project

Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/biosigner.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/biosigner).

## Description

**Version:** 2.2.2  
**Date:** 2016-05-21  
**Author:** Philippe Rinaudo and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)   
**Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)  
**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.   
**Licence:** CeCILL
**Reference history:** [W4M00003_diaplasma](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 file: `biosigner_config.xml`.
* Image files: 
  + `static/images/biosigner_workflowPositionImage.png`.   
  + `static/images/biosigner_workingExampleImage.png`.
* Wrapper file: `biosigner_wrapper.R`.
* R packages  
  + **batch** from CRAN: `install.packages("batch", dep=TRUE)`.
  + **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")`.

## Tests

The code in the wrapper can be tested by running the `tests/biosigner_tests.R` in R  

## News

## CHANGES IN VERSION 2.2.2

 * 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)
    
## CHANGES IN VERSION 2.2.1

 * Creation of the tool: with S3 versions of biosigner (< 1.0.0) and ropls (< 1.4.0)