Mercurial > repos > ethevenot > biosigner

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

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

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

### Description

**Version:** 2.2.6
**Date:** 2016-08-05
**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

    ```r
    install.packages("batch", dep=TRUE)
    ```
  + **biosigner** from Bioconductor

    ```r
    source("http://www.bioconductor.org/biocLite.R")
    biocLite("biosigner")
    ```

### Tests

The code in the wrapper can be tested by running the `runit/biosigner_runtests.R` R file

You will need to install **RUnit** package in order to make it run:
```r
install.packages('RUnit', dependencies = TRUE)
```

### Working example

See the **W4M00001a_sacurine-subset-statistics** or **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)

### News

###### CHANGES IN VERSION 2.2.6

INTERNAL MODIFICATION

 * Minor internal modifications

###### CHANGES IN VERSION 2.2.4

INTERNAL MODIFICATION

 * Internal updates for planemo and travis validation

###### CHANGES IN VERSION 2.2.2

INTERNAL MODIFICATION

 * 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

NEW FEATURE

 * Creation of the tool: with S3 versions of biosigner (< 1.0.0) and ropls (< 1.4.0)
author	ethevenot
date	Sat, 06 Aug 2016 12:17:12 -0400
parents	4ff502a46189
children