shinyDepMap

A shiny-based interactive web tool to analyze DepMap data (based on their 19q3 release). There are several options for using it:

1. Use the public version of the tool
2. Run the tool locally in R
3. Run the tool locally using Docker

Run with R

Preparation

To launch this tool locally in R, clone or download this repository and install the required R pacakges as follows:

install.packages("devtools")
install.packages("BiocManager")

BiocManager::install(c("ggplot2","shiny","markdown","RColorBrewer","shinyWidgets","plotly","DT","igraph","visNetwork","tibble","shinyjs","dplyr","tidyr","yonder"))

Launch the app

In the R process, modify the path to the parent directory of the source directory and run the code.

library(shiny)
setwd("/_the_parent_dir_of_the_source_dir_/")
runApp("shinyDepMap")

Run with Docker

(to be implemented)
An alternative to the _Run with R_ option. Run the following commands, then open
your web browser to http://127.0.0.1:8888/ .

```
docker pull labsyspharm/shinydepmap:latest
docker run -p 8888:8888 labsyspharm/shinydepmap:latest
```

Bug reports

Please contact Kenichi Shimada in case you find a bug.

Version history

The current version is v2.0. The older version (v1.0) can be found in the depmap_flexdashboard branch of this repo.

Session info

R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] yonder_0.2.0       markdown_1.1       tidyr_0.8.3        dplyr_0.8.3       
 [5] tibble_2.1.3       visNetwork_2.0.8   igraph_1.2.4.1     DT_0.8            
 [9] plotly_4.9.0       shinyWidgets_0.4.8 RColorBrewer_1.1-2 ggplot2_3.2.1     
[13] shiny_1.4.0       

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2        pillar_1.4.2      compiler_3.6.1    later_1.0.0      
 [5] tools_3.6.1       digest_0.6.21     viridisLite_0.3.0 jsonlite_1.6     
 [9] gtable_0.3.0      pkgconfig_2.0.3   rlang_0.4.0       crosstalk_1.0.0  
[13] yaml_2.2.0        xfun_0.9          fastmap_1.0.1     withr_2.1.2      
[17] httr_1.4.1        htmlwidgets_1.3   grid_3.6.1        tidyselect_0.2.5 
[21] glue_1.3.1        data.table_1.12.2 R6_2.4.0          purrr_0.3.2      
[25] magrittr_1.5      scales_1.0.0      promises_1.1.0    htmltools_0.4.0  
[29] assertthat_0.2.1  mime_0.7          xtable_1.8-4      colorspace_1.4-1 
[33] httpuv_1.5.2      lazyeval_0.2.2    munsell_0.5.0     crayon_1.3.4