pack03.packages.R

################################################################################
#                                PACKAGES TO LOAD                              #
################################################################################

install.packages.auto("readr")
install.packages.auto("optparse")
install.packages.auto("tools")
install.packages.auto("dplyr")
install.packages.auto("tidyr")
install.packages.auto("tidylog")
library("tidylog", warn.conflicts = FALSE)
install.packages.auto("naniar")

# To get 'data.table' with 'fwrite' to be able to directly write gzipped-files
# Ref: https://stackoverflow.com/questions/42788401/is-possible-to-use-fwrite-from-data-table-with-gzfile
# install.packages("data.table", repos = "https://Rdatatable.gitlab.io/data.table")
library(data.table)

install.packages.auto("tidyverse")
install.packages.auto("knitr")
install.packages.auto("DT")

install.packages.auto("org.Hs.eg.db")
install.packages.auto("mygene")
install.packages.auto("EnhancedVolcano")

install.packages.auto("haven")
install.packages.auto("tableone")

# For a more efficient implementation of the Wilcoxon Rank Sum Test,
# (default method for FindMarkers) please install the limma package
# --------------------------------------------
install.packages.auto('BiocManager')
BiocManager::install('limma')
# --------------------------------------------
#   After installation of limma, Seurat will automatically use the more 
# efficient implementation (no further action necessary).
# This message will be shown once per session

# Install the devtools package from Hadley Wickham
install.packages.auto('devtools')
# Replace '2.3.4' with your desired version
# devtools::install_version(package = 'Seurat', version = package_version('2.3.4'))
install.packages.auto("Seurat")
library("Seurat")