Mercurial > repos > ethevenot > heatmap
comparison README.md @ 0:ad06aeed02c9 draft
planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
| author | ethevenot |
|---|---|
| date | Tue, 02 Aug 2016 06:26:41 -0400 |
| parents | |
| children | db1d80e89156 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:ad06aeed02c9 |
|---|---|
| 1 ## Heatmap of the data matrix | |
| 2 #### A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project | |
| 3 | |
| 4 Status: [](https://travis-ci.org/workflow4metabolomics/heatmap). | |
| 5 | |
| 6 ### Description | |
| 7 | |
| 8 **Version:** 2.2.0 | |
| 9 **Date:** 2016-07-30 | |
| 10 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) | |
| 11 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) | |
| 12 **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) | |
| 13 **Licence:** CeCILL | |
| 14 **Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published) | |
| 15 **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) | |
| 16 | |
| 17 ### Installation | |
| 18 | |
| 19 * Configuration file: **heatmap_config.xml** | |
| 20 * Image files: | |
| 21 + **static/images/heatmap_workflowPositionImage.png** | |
| 22 + **static/images/heatmap_workingExampleImage.png** | |
| 23 * Wrapper file: **heatmap_wrapper.R** | |
| 24 * R packages | |
| 25 + **batch** from CRAN | |
| 26 > install.packages("batch", dep=TRUE) | |
| 27 | |
| 28 ### Tests | |
| 29 | |
| 30 The code in the wrapper can be tested by running the **tests/heatmap_tests.R** in R | |
| 31 | |
| 32 ### News | |
| 33 | |
| 34 ##### CHANGES IN VERSION 2.2.0 | |
| 35 | |
| 36 NEW FEATURES | |
| 37 | |
| 38 o Default method for the correlation coefficient is now 'pearson', instead of 'spearman' previously (the latter can still be selected in the advanced parameters) | |
| 39 | |
| 40 o 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 | |
| 41 | |
| 42 o A new red-green color scale is available | |
| 43 | |
| 44 *** | |
| 45 | |
| 46 ##### CHANGES IN VERSION 2.1.2 | |
| 47 | |
| 48 INTERNAL MODIFICATION | |
| 49 | |
| 50 o Creating additional files for planemo and travis validation | |
| 51 | |
| 52 *** | |
| 53 | |
| 54 ##### CHANGES IN VERSION 2.0.2 | |
| 55 | |
| 56 INTERNAL MODIFICATION | |
| 57 | |
| 58 o Creating tests for R code | |
| 59 | |
| 60 *** |