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planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 957d0e442c875f7cf8461866fac9695175ab371b
author ethevenot
date Wed, 28 Feb 2018 06:22:18 -0500
parents 75a031fa583d
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ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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1 Univariate parametric and non-parametric hypothesis testing with correction for multiple testing
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2 ================================================================================================
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4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
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6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/univariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/univariate).
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8 ### Description
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10 **Version:** 2.2.4
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11 **Date:** 2018-01-11
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12 **Author:** Marie Tremblay-Franco (INRA, MetaToul, MetaboHUB, W4M Core Development Team) and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
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13 **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)
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14 **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)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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15 **Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00004_mtbls1](http://galaxy.workflow4metabolomics.org/history/list_published)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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16 **Licence:** CeCILL
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17 **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)
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19 ### Installation
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21 * Configuration file: `univariate_config.xml`
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22 * Image file:
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23 + `static/images/univariate_workflowPositionImage.png`
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24 * Wrapper file: `univariate_wrapper.R`
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25 * Script file: `univariate_script.R`
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26 * R packages
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27 + **batch** from CRAN
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29 ```r
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30 install.packages("batch", dep=TRUE)
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31 ```
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32 + **PMCMR** from CRAN
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34 ```r
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35 install.packages("PMCMR", dep=TRUE)
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36 ```
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ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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38 ### Tests
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40 The code in the wrapper can be tested by running the `runit/univariate_runtests.R` R file
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42 You will need to install **RUnit** package in order to make it run:
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43 ```r
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44 install.packages('RUnit', dependencies = TRUE)
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45 ```
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47 ### Working example
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49 See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-subset-complete**, **W4M00002_mtbls2**, **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
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51 ### News
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53 ###### CHANGES IN VERSION 2.2.4
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55 MINOR MODIFICATION
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57 * Internal minor modifications for building and testing
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59 ###### CHANGES IN VERSION 2.2.0
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61 MAJOR MODIFICATION
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63 * ANOVA and Kruskal-Wallis: The p-values of the post-hoc tests (i.e. from pairwise comparisons) are now further corrected for multiple testing over all variables (previously, only the p-value of the -first- omnibus test was corrected over all variables)
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65 MINOR MODIFICATION
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67 * All values in the 'dif', adjusted p-value, and 'sig' columns are now displayed (previously, the values were set to NA when the p-value of the omnibus test was not significant)
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69 NEW FEATURE
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71 * Graphic: a single pdf file containing the graphics of all significant tests is now produced as '_figure.pdf' output: boxplots (respectively scatterplots with the regression line in red and the R2 value) are displayed when the factor of interest is qualitative (respectively quantitative). The corrected p-value is indicated in the title of each plot
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73 ###### CHANGES IN VERSION 2.1.4
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75 NEW FEATURE
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77 * Level names are now separated by '.' instead of '-' previously in the column names of the output variableMetadata table (e.g., 'jour_ttest_J3.J10_fdr' instead of 'jour_ttest_J3-J10_fdr' previously)
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79 INTERNAL MODIFICATION
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81 * Minor internal changes
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83 ###### CHANGES IN VERSION 2.1.2
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85 INTERNAL MODIFICATION
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87 * Minor internal changes in .shed.yml for toolshed export
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89 ###### CHANGES IN VERSION 2.1.1
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90
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
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91 INTERNAL MODIFICATION
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
diff changeset
92
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
diff changeset
93 * Internal handling of 'NA' p-values (e.g. when intensities are identical in all samples).