R Session Info

For the main R packages that I used in this analysis see: (Wang and Song 2011), (Gu 2019), (Gu, Eils, and Schlesner 2016), (Zobolas 2019 b), (Zobolas 2019 a).

A very useful tutorial about network visualization in R: (Ognyanova 2019)

For adding code folding buttons in bookdown::gitbook see (S 2017).

I also provide for reproducibity purposes the information about the R session that is used throughout this bookdown document:

xfun::session_info()

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Locale:
  LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
  LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
  LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
  LC_PAPER=en_US.UTF-8       LC_NAME=C                 
  LC_ADDRESS=C               LC_TELEPHONE=C            
  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

Package version:
  assertthat_0.2.1     backports_1.1.5      base64enc_0.1.3     
  BH_1.69.0.1          bibtex_0.4.2         bookdown_0.14       
  circlize_0.4.8       Ckmeans.1d.dp_4.3.0  cli_1.1.0           
  clue_0.3-57          cluster_2.1.0        colorspace_1.4-1    
  compiler_3.6.1       ComplexHeatmap_2.0.0 crayon_1.3.4        
  digest_0.6.21        dplyr_0.8.3          ellipsis_0.3.0      
  emba_0.1.1           evaluate_0.14        fansi_0.4.0         
  gbRd_0.4-11          GetoptLong_0.1.7     GlobalOptions_0.1.1 
  glue_1.3.1           graphics_3.6.1       grDevices_3.6.1     
  grid_3.6.1           highr_0.8            htmltools_0.4.0     
  htmlwidgets_1.5.1    igraph_1.2.4.1       jsonlite_1.6        
  knitr_1.25           lattice_0.20.38      magrittr_1.5        
  markdown_1.1         Matrix_1.2.17        methods_3.6.1       
  mime_0.7             parallel_3.6.1       pillar_1.4.2        
  pkgconfig_2.0.3      plogr_0.2.0          png_0.1-7           
  purrr_0.3.2          R6_2.4.0             RColorBrewer_1.1-2  
  Rcpp_1.0.2           Rdpack_0.11-0        rje_1.10.10         
  rjson_0.2.20         rlang_0.4.0          rmarkdown_1.16      
  shape_1.4.4          stats_3.6.1          stringi_1.4.3       
  stringr_1.4.0        tibble_2.1.3         tidyselect_0.2.5    
  tinytex_0.16         tools_3.6.1          usefun_0.4.1        
  utf8_1.1.4           utils_3.6.1          vctrs_0.2.0         
  visNetwork_2.0.8     xfun_0.10            yaml_2.2.0          
  zeallot_0.1.0