Add instructions and validate that all libraries loaded correctly

setup/install_dependencies.R

+source("~/.Rprofile")
+
+if (!requireNamespace("BiocManager", quietly = TRUE))
+  install.packages("BiocManager")
+
+BiocManager::install()
+BiocManager::install(c("enrichplot"))
+BiocManager::install(c("topGO"))
+BiocManager::install(c("clusterProfiler"))
+BiocManager::install(c("ReactomePA"))
+BiocManager::install(c("AnnotationDbi"))
+BiocManager::install(c("STRINGdb"))
+BiocManager::install(c("pathview"))
+BiocManager::install(c("org.Hs.eg.db"))
+BiocManager::install(c("org.Mm.eg.db"))
+BiocManager::install(c("biomaRt"))
+BiocManager::install(c("igraph"))
+
+install.packages(c("ggupset", "dplyr", "plyr", "reshape", "reshape2", "devtools", "tidyverse", "httr", "jsonlite", "RJSONIO", "pathfindR"))
+
+# Install also doseplot directly from the developer:
+library(devtools)
+devtools::install_github(c("GuangchuangYu/doseplot"))
+
+# if your system has trouble installing reactomePA, clusterProfiler, DOSE or pathfindR, please try the developer versions:
+devtools::install_github(c("GuangchuangYu/clusterProfiler", "GuangchuangYu/ReactomePA", "GuangchuangYu/DOSE", "egeulgen/pathfindR"))
+
+# After installation, check all libraries by loading them into the environment.
+# For those installed via devtools use the package name only - e.g. library("DOSE")
+
+# If you encounter problems installing the above and you can't find a solution, consider installing R 4.0.3 and their dependencies using https://bioconda.github.io/
+# With exception of "pathfindR", all packages are available from bioconda and conda-forge channels as "bioconductor-..." or "r-...".
+# Install "pathfindR" after all others with "devtools::install_github(c("egeulgen/pathfindR"))" 

setup/validate_dependencies.R

+source("~/.Rprofile")
+
+suppressWarnings(suppressMessages(library("AnnotationDbi")))
+suppressWarnings(suppressMessages(library("DOSE")))
+suppressWarnings(suppressMessages(library("RJSONIO")))
+suppressWarnings(suppressMessages(library("ReactomePA")))
+suppressWarnings(suppressMessages(library("STRINGdb")))
+suppressWarnings(suppressMessages(library("biomaRt")))
+suppressWarnings(suppressMessages(library("clusterProfiler")))
+suppressWarnings(suppressMessages(library("devtools")))
+suppressWarnings(suppressMessages(library("doseplot")))
+suppressWarnings(suppressMessages(library("dplyr")))
+suppressWarnings(suppressMessages(library("enrichplot")))
+suppressWarnings(suppressMessages(library("ggupset")))
+suppressWarnings(suppressMessages(library("httr")))
+suppressWarnings(suppressMessages(library("igraph")))
+suppressWarnings(suppressMessages(library("jsonlite")))
+suppressWarnings(suppressMessages(library("org.Hs.eg.db")))
+suppressWarnings(suppressMessages(library("org.Mm.eg.db")))
+suppressWarnings(suppressMessages(library("pathfindR")))
+suppressWarnings(suppressMessages(library("pathview")))
+suppressWarnings(suppressMessages(library("plyr")))
+suppressWarnings(suppressMessages(library("reshape")))
+suppressWarnings(suppressMessages(library("reshape2")))
+suppressWarnings(suppressMessages(library("tidyverse")))
+suppressWarnings(suppressMessages(library("topGO")))
+
+cat("If you didn't see any error message, you are good to go\n")