Mercurial > repos > ethevenot > heatmap
comparison README.md @ 0:81ffd91ba495 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit bbfc13f2e4fa9e7e5b562c96d0e570318d3482d9
| author | ethevenot |
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| date | Tue, 24 Oct 2017 09:32:23 -0400 |
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| 1 Heatmap of the data matrix | |
| 2 ========================== | |
| 3 | |
| 4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure | |
| 5 | |
| 6 Status: [](https://travis-ci.org/workflow4metabolomics/heatmap). | |
| 7 | |
| 8 ### Description | |
| 9 | |
| 10 **Version:** 2.2.2 | |
| 11 **Date:** 2016-08-04 | |
| 12 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) | |
| 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) | |
| 15 **Licence:** CeCILL | |
| 16 **Reference history:** [W4M00001a_sacurine-subset-statistics](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) | |
| 18 | |
| 19 ### Installation | |
| 20 | |
| 21 * Configuration file: `heatmap_config.xml` | |
| 22 * Image files: | |
| 23 + `static/images/heatmap_workflowPositionImage.png` | |
| 24 + `static/images/heatmap_workingExampleImage.png` | |
| 25 * Wrapper file: `heatmap_wrapper.R` | |
| 26 * R packages | |
| 27 + **batch** from CRAN | |
| 28 | |
| 29 ```r | |
| 30 install.packages("batch", dep=TRUE) | |
| 31 ``` | |
| 32 | |
| 33 ### Tests | |
| 34 | |
| 35 The code in the wrapper can be tested by running the `runit/heatmap_runtests.R` R file | |
| 36 | |
| 37 ### Working example | |
| 38 | |
| 39 See the **W4M00001a_sacurine-subset-statistics** shared history in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published) | |
| 40 | |
| 41 ### News | |
| 42 | |
| 43 ##### CHANGES IN VERSION 2.2.2 | |
| 44 | |
| 45 INTERNAL MODIFICATION | |
| 46 | |
| 47 * Minor internal modifications | |
| 48 | |
| 49 ##### CHANGES IN VERSION 2.2.0 | |
| 50 | |
| 51 NEW FEATURES | |
| 52 | |
| 53 * Default method for the correlation coefficient is now 'pearson', instead of 'spearman' previously (the latter can still be selected in the advanced parameters) | |
| 54 | |
| 55 * The 1-abs(correlation) dissimilarity is now available (in addition to the default '1-correlation') in case the sign of correlations between samples and between variables does not matter, as well as the euclidean, maximum, manhattan, canberra, binary, and minkowski dissimilarities | |
| 56 | |
| 57 * A new red-green color scale is available | |
| 58 | |
| 59 ##### CHANGES IN VERSION 2.1.2 | |
| 60 | |
| 61 INTERNAL MODIFICATION | |
| 62 | |
| 63 * Creating additional files for planemo and travis validation | |
| 64 | |
| 65 ##### CHANGES IN VERSION 2.0.2 | |
| 66 | |
| 67 INTERNAL MODIFICATION | |
| 68 | |
| 69 * Creating tests for R code |