Mercurial > repos > eschen42 > multivariate
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
| author | eschen42 |
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| date | Mon, 14 Aug 2017 20:57:59 -0400 |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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1 Multivariate analysis by PCA, PLS(-DA), and OPLS(-DA) |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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2 ===================================================== |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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3 |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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5 |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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6 Status: [](https://travis-ci.org/workflow4metabolomics/multivariate). |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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7 |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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8 ### Description |
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9 |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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10 **Version:** 2.3.8 |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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11 **Date:** 2016-10-21 |
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12 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) |
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13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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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) |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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15 **Licence:** CeCILL |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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16 **Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00001b_sacurine_complete](http://galaxy.workflow4metabolomics.org/history/list_published) |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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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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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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18 |
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19 ### Installation |
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20 |
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21 * Configuration file: `multivariate_config.xml` |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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22 * Image files: |
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23 + `static/images/multivariate_workflowPositionImage.png` |
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24 + `static/images/multivariate_workingExampleImage.png` |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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25 * Wrapper file: `multivariate_wrapper.R` |
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26 * R packages |
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27 + **batch** from CRAN |
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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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28 |
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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 |
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33 + **ropls** from Bioconductor |
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34 |
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35 ```r |
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36 source("http://www.bioconductor.org/biocLite.R") |
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37 biocLite("ropls") |
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38 ``` |
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39 |
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40 ### Tests |
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41 |
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42 The code in the wrapper can be tested by running the `runit/multivariate_runtests.R` R file |
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43 |
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44 You will need to install **RUnit** package in order to make it run: |
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45 ```r |
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46 install.packages('RUnit', dependencies = TRUE) |
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47 ``` |
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48 |
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49 ### Working example |
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50 |
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51 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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52 |
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53 ### News |
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54 |
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55 ###### CHANGES IN VERSION 2.3.8 |
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56 |
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57 MINOR MODIFICATION |
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58 |
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59 * (O)PLS(-DA) coefficients display in case of multiple quantitative (or multiclass) response: now the column names of the coefficients for each response are correctly labelled in the variableMetadata file |
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60 |
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61 ###### CHANGES IN VERSION 2.3.6 |
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62 |
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63 INTERNAL MODIFICATION |
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64 |
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65 * minor internal modifications |
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66 |
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67 ###### CHANGES IN VERSION 2.3.4 |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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68 |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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69 INTERNAL MODIFICATION |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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70 |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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71 * minor update of .shed.yml |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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72 |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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73 ###### CHANGES IN VERSION 2.3.2 |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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74 |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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75 INTERNAL MODIFICATION |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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76 |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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77 * Modification of the `multivariate_wrapper.R` file to handle **ropls** package versions of 1.3.15 and above (i.e. after switching to S4 classes) |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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78 |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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79 ###### CHANGES IN VERSION 2.3.0 |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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80 |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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81 NEW FEATURES |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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82 |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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83 * **Predictions** now available (see the 'Samples to be tested' argument) |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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84 * OPLS(-DA): **Predictive and Orthogonal VIP** are now computed (see the 'comments' section) |
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b2b02fb81a0a
planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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85 * **Multiclass PLS-DA** implemented (see the 'comments' section) |