The code in the repository allows reproducing all the findings and all the figures that are presented in the published manuscript.
license: CC BY 4.0
All the code was developed for R.
It is recommended, to obtain all the plots, to run the command from the R command line with the following syntax:
source("scriptName.R", print.eval=T)
or from RStudio using Source with Echo or Shift+Ctrl+Enter.
This is sessionInfo() loaded from the 03_results_analysis.R script.
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=it_IT.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] extrafont_0.17 igraph_1.2.6 RColorBrewer_1.1-2 ggrepel_0.9.1
[5] UpSetR_1.4.0 reshape2_1.4.4 ggplot2_3.3.3
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 pillar_1.5.1 compiler_4.1.0 plyr_1.8.6
[5] tools_4.1.0 lifecycle_1.0.0 tibble_3.1.0 gtable_0.3.0
[9] pkgconfig_2.0.3 rlang_0.4.10 DBI_1.1.1 Rttf2pt1_1.3.8
[13] gridExtra_2.3 withr_2.4.1 dplyr_1.0.5 stringr_1.4.0
[17] generics_0.1.0 vctrs_0.3.6 tidyselect_1.1.0 glue_1.4.2
[21] R6_2.5.0 fansi_0.4.2 purrr_0.3.4 extrafontdb_1.0
[25] magrittr_2.0.1 scales_1.1.1 ellipsis_0.3.1 assertthat_0.2.1
[29] colorspace_2.0-0 utf8_1.2.1 stringi_1.5.3 munsell_0.5.0
[33] crayon_1.4.1
STRING database v11 was used to obtain protein-protein interactions information.
Experimental only interactions were considered.
Medium confidence, i.e. 400+, threshold was used since its STRING's default.