Mercurial > repos > ethevenot > biosigner
diff README.md @ 0:48e4be935243 draft
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
author | ethevenot |
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date | Wed, 27 Jul 2016 11:40:20 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Jul 27 11:40:20 2016 -0400 @@ -0,0 +1,42 @@ +Discovery of significant signatures from omics data +=================================================== + +A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project + +Status: [](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)