Bioconductor Code: bioCancer (original) (raw)

# bioCancer - Interactive Multi-OMICS Cancers Data Visualization and Analysis [\](https://travis-ci.org/kmezhoud/bioCancer) [\](https://bioconductor.org/packages/bioCancer) [\](https://github.com/bioCancer) [\](https://www.bioconductor.org/packages/devel/bioc/html/bioCancer.html#since) [\](https://bioconductor.org/packages/stats/bioc/bioCancer) [bioCancer]( http://kmezhoud.github.io/bioCancer/ ) is a browser-based interface for Cancer Genomics Data analysis and visualization developped by [R](http://www.r-project.org/), and based on the [Shiny](http://www.rstudio.com/shiny/) package. Example of bioCancer server is hosted at http://46.101.227.???:3838/bioCancer/ #### Interactivities bioCancer is listening user setting. Results are updated immediately when inputs are changed (i.e., no separate dialog boxes). #### Context bioCancer focuses on Cancer Genomics data visualisation and Genes Classifications. ## Circomics: Pull User genetic profiles with existing Cancer studies ## Preprocessing and Plotting ## Genes Classification and Biological terms Clustering ## Network modeling example ## How to install bioCancer - Required: [R](http://cran.rstudio.com/) version 3.2 or later - Required: A modern browser (e.g., [Chrome](https://www.google.com/intl/en/chrome/browser/desktop/) or Safari). Internet Explorer (version 11 or higher) should work as well - Recommended: [Rstudio](http://www.rstudio.com/products/rstudio/download/) bioCancer courant release: ```r if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("bioCancer") ``` bioCancer is under development: ```r devtools::install_github("kmezhoud/bioCancer") library("bioCancer") ``` When bioCancer starts you will see a table of available Cancer Studies. To close the application click on `Quit` in the Navigation bar and then click the `Quit` button on the left of the screen. The bioCancer process will stop and the browser window will close (or gray-out). ## Documentation Documentation and tutorials are available in the bioCancer web interface (the `?` icons and the `Help` menu). ## Acknowledgment bioCancer is a collaborative work . Processing panel is adapted from [radiant](https://github.com/vnijs/radiant). I would like to thank Dr. Vincent Nijs for sharing his work for R community.