Discovery of significant signatures from omics data

A Galaxy module from the Workflow4metabolomics infrastructure

Status: .

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
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
Funding: Agence Nationale de la Recherche (MetaboHUB 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

  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:

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)