Mercurial > repos > ethevenot > multivariate
comparison README.md @ 2:fa173e12e185 draft
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
author | ethevenot |
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date | Sat, 06 Aug 2016 12:07:13 -0400 |
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1 Multivariate analysis by PCA, PLS(-DA), and OPLS(-DA) | 1 Multivariate analysis by PCA, PLS(-DA), and OPLS(-DA) |
2 ===================================================== | 2 ===================================================== |
3 | 3 |
4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project | 4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure |
5 | 5 |
6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/multivariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/multivariate). | 6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/multivariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/multivariate). |
7 | 7 |
8 ## Description | 8 ### Description |
9 | 9 |
10 **Version:** 2.3.4 | 10 **Version:** 2.3.6 |
11 **Date:** 2016-07-30 | 11 **Date:** 2016-08-05 |
12 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) | 12 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) |
13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) | 13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) |
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) | 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) |
15 **Licence:** CeCILL | 15 **Licence:** CeCILL |
16 **Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00001b_sacurine_complete](http://galaxy.workflow4metabolomics.org/history/list_published) | 16 **Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00001b_sacurine_complete](http://galaxy.workflow4metabolomics.org/history/list_published) |
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) | 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) |
18 | 18 |
19 ## Installation | 19 ### Installation |
20 | 20 |
21 * Configuration file: `multivariate_config.xml`. | 21 * Configuration file: `multivariate_config.xml` |
22 * Image files: | 22 * Image files: |
23 + `static/images/multivariate_workflowPositionImage.png`. | 23 + `static/images/multivariate_workflowPositionImage.png` |
24 + `static/images/multivariate_workingExampleImage.png`. | 24 + `static/images/multivariate_workingExampleImage.png` |
25 * Wrapper file: `multivariate_wrapper.R`. | 25 * Wrapper file: `multivariate_wrapper.R` |
26 * R packages | 26 * R packages |
27 + **batch** from CRAN | 27 + **batch** from CRAN |
28 | 28 |
29 ```r | 29 ```r |
30 install.packages("batch", dep=TRUE) | 30 install.packages("batch", dep=TRUE) |
35 ```r | 35 ```r |
36 source("http://www.bioconductor.org/biocLite.R") | 36 source("http://www.bioconductor.org/biocLite.R") |
37 biocLite("ropls") | 37 biocLite("ropls") |
38 ``` | 38 ``` |
39 | 39 |
40 ## Tests | 40 ### Tests |
41 | 41 |
42 The code in the wrapper can be tested by running the `tests/multivariate_tests.R` in R. | 42 The code in the wrapper can be tested by running the `runit/multivariate_runtests.R` R file |
43 | 43 |
44 You will need to install **RUnit** package in order to make it run: | 44 You will need to install **RUnit** package in order to make it run: |
45 ```r | 45 ```r |
46 install.packages('RUnit', dependencies = TRUE) | 46 install.packages('RUnit', dependencies = TRUE) |
47 ``` | 47 ``` |
48 | 48 |
49 ## News | 49 ### Working example |
50 | 50 |
51 ### CHANGES IN VERSION 2.3.4 | 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) |
52 | |
53 ### News | |
54 | |
55 ###### CHANGES IN VERSION 2.3.6 | |
56 | |
57 INTERNAL MODIFICATION | |
58 | |
59 * minor internal modifications | |
60 | |
61 ###### CHANGES IN VERSION 2.3.4 | |
52 | 62 |
53 INTERNAL MODIFICATION | 63 INTERNAL MODIFICATION |
54 | 64 |
55 * minor update of .shed.yml | 65 * minor update of .shed.yml |
56 | |
57 *** | |
58 | 66 |
59 ### CHANGES IN VERSION 2.3.2 | 67 ###### CHANGES IN VERSION 2.3.2 |
60 | 68 |
61 INTERNAL MODIFICATION | 69 INTERNAL MODIFICATION |
62 | 70 |
63 * 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). | 71 * 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) |
64 | |
65 *** | |
66 | 72 |
67 ### CHANGES IN VERSION 2.3.0 | 73 ###### CHANGES IN VERSION 2.3.0 |
68 | 74 |
69 NEW FEATURES | 75 NEW FEATURES |
70 | 76 |
71 * **Predictions** now available (see the 'Samples to be tested' argument). | 77 * **Predictions** now available (see the 'Samples to be tested' argument) |
72 * OPLS(-DA): **Predictive and Orthogonal VIP** are now computed (see the 'comments' section). | 78 * OPLS(-DA): **Predictive and Orthogonal VIP** are now computed (see the 'comments' section) |
73 * **Multiclass PLS-DA** implemented (see the 'comments' section). | 79 * **Multiclass PLS-DA** implemented (see the 'comments' section) |
74 | |
75 *** |