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README.md

If you use SmartR in your publication please cite it:

https://doi.org/10.1093/bioinformatics/btx137

###SmartR is a grails plugin seeking to improve the visual analytics of the tranSMART platform by using recent web technologies such as d3.

Heatmap Example

Installation

tranSMART 16.2, eTRIKS v3 and younger builds

SmartR will be included by default. No modification necessary.

tranSMART 1.2.5 and 16.1
  1. Add runtime ':smart-r:1.0-STABLE-SNAPSHOT' to BuildConfig.groovy in the transmartApp source code.
  2. Compile a WAR file via grails war for deployment.
tranSMART 1.2.4 and older
  1. Add runtime ':smart-r:1.0-STABLE-SNAPSHOT' to BuildConfig.groovy in the transmartApp source code.
  2. Add the following code to transmartApp/web-app/js/datasetExplorer/datasetExplorer.js near >>this location<< :
    resultsTabPanel.insert(4, smartRPanel);
})```
3. Compile a WAR file via ```grails war``` for deployment.

#### Requirements
- SmartR requires the following R packages:
  - [jsonlite](https://cran.r-project.org/web/packages/jsonlite/index.html)
  - [gplots](https://cran.r-project.org/web/packages/gplots/index.html)
  - [reshape2](https://cran.r-project.org/web/packages/reshape2/index.html)
  - [WGCNA](https://cran.r-project.org/web/packages/WGCNA/index.html)
  - [limma](https://bioconductor.org/packages/release/bioc/html/limma.html)
  - [zoo](https://cran.r-project.org/web/packages/zoo/index.html)
  
#### Releases
- https://github.com/transmart/SmartR/releases

#### Wiki
- https://wiki.transmartfoundation.org/display/transmartwiki/SmartR