Mercurial > repos > ethevenot > univariate
diff README.md @ 0:ef64d3752050 draft
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
author | ethevenot |
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date | Wed, 27 Jul 2016 11:44:34 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Jul 27 11:44:34 2016 -0400 @@ -0,0 +1,37 @@ +# Univariate parametric and non-parametric hypothesis testing with correction for multiple testing + +A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project. + +Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/univariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/univariate). + +## Description + +**Version:** 2.1.1 +**Date:** 2015-09-30 +**Author:** Marie Tremblay-Franco (INRA, MetaToul, MetaboHUB, W4M Core Development Team) and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) +**Email:** [marie.tremblay-franco(at)toulouse.inra.fr](mailto:marie.tremblay-franco@toulouse.inra.fr); [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) +**Citation:** Thevenot E.A., Roux A., Xu Y., Ezan E. and Junot C. (2015). Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. *Journal of Proteome Research*, **14**:3322-3335. [doi:10.1021/acs.jproteome.5b00354](http://dx.doi.org/10.1021/acs.jproteome.5b00354) +**Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00004_mtbls1](http://galaxy.workflow4metabolomics.org/history/list_published) +**Licence:** CeCILL +**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: **univariate_config.xml** + * Image file: + + **static/images/univariate_workflowPositionImage.png** + * Wrapper file: **univariate_wrapper.R** + * Script file: **univariate_script.R** + * R packages + + **batch** from CRAN: `install.packages("batch", dep=TRUE)`. + + **PMCMR** from Bioconductor: `install.packages("PMCMR", dep=TRUE)`. + +## Tests + +The code in the wrapper can be tested by running the **tests/univariate_tests.R** in R + +## News + +## CHANGES IN VERSION 2.1.1 + + * Internal handling of 'NA' p-values (e.g. when intensities are identical in all samples).