polish installation notes

workflows/_dependencies/install_r_packages.R

-#!/usr/bin/env Rscript
-
-########################
-# Installation of R dependencies
-########################
-
-### sleuth installation
-
-if (!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")}
-if(!"BiocManager" %in% row.names(installed.packages())){BiocManager::install()}
-if(!"devtools" %in% row.names(installed.packages())){BiocManager::install("devtools")}
-
-# BiocManager::install("pachterlab/sleuth")
-# There's currently (early 2022) an issue with sleuth installation. 
-# Using this workaround from https://github.com/pachterlab/sleuth/issues/259#issuecomment-1001076030
-
-if(!"sleuth" %in% row.names(installed.packages())){remotes::install_github("pachterlab/sleuth#260")}
-
-library(sleuth)
-
-### other packages
-
-library(tidyverse)
-library(jsonlite)
-library(openxlsx)
-
-required_packages <- 
-  c('tidyverse',  ## data wrangling and plotting
-    'jsonlite',   ## read/write json files
-    'openxlsx')   ## read/write xlsx files
-
-for(package in required_packages)
-{
-  ## Check if package is installed. If not, install
-  if(!package %in% row.names(installed.packages())){install.packages(package,
-                                                                     repos ="https://cran.uni-muenster.de/")}
-  # ## Check if package is up to date. If not, update
-  # update.packages(package, repos = "https://cran.uni-muenster.de/")
-  ## Load package
-  library(package, character.only = T)
-  print(paste("installed R package", package))
-}
-

workflows/install_dependencies/install_r_packages.R

+#!/usr/bin/env Rscript
+
+################################################
+### Installation of R dependencies #############
+################################################
+
+### Default (CRAN)
+
+if(!"tidyverse" %in% row.names(installed.packages())){install.packages("tidyverse")}
+if(!"jsonlite" %in% row.names(installed.packages())){install.packages("jsonlite")}
+if(!"openxlsx" %in% row.names(installed.packages())){install.packages("openxlsx")}
+if(!"kableExtra" %in% row.names(installed.packages())){install.packages("kableExtra")}
+if(!"shiny" %in% row.names(installed.packages())){install.packages("shiny")}
+if(!"RColorBrewer" %in% row.names(installed.packages())){install.packages("RColorBrewer")}
+
+### From BiocManager
+
+if (!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")}
+if(!"BiocManager" %in% row.names(installed.packages())){BiocManager::install()}
+if(!"devtools" %in% row.names(installed.packages())){BiocManager::install("devtools")}
+if(!"sleuth" %in% row.names(installed.packages())){BiocManager::install("pachterlab/sleuth")}
+
+### Test load packages
+
+library(tidyverse)
+library(jsonlite)
+library(openxlsx)
+library(sleuth)
+library(kableExtra)
+library(shiny)
+library(RColorBrewer)