setup_r_env.R

# CRAN
install.packages("devtools", dependencies = T)
library("devtools")
if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager", dependencies = T)
install.packages("tidyverse", dependencies = T)
install.packages("data.table", dependencies = T)
install.packages("RColorBrewer", dependencies = T)
install.packages("VennDiagram", dependencies = T)
install.packages("pheatmap", dependencies = T)
install.packages("remote", dependencies = T)
install.packages("jsonlite", dependencies = T)
install.packages("purrr", dependencies = T)
install.packages("httr", dependencies = T)
install.packages("xml2", dependencies = T)
install.packages("dplyr", dependencies = T)

# Bioconductor
BiocManager::install("liftOver")
BiocManager::install("plyranges")
BiocManager::install("GenomicRanges")
BiocManager::install("rtracklayer")
BiocManager::install("DESeq2")
BiocManager::install("biomaRt")

# Other
install_github('lukaswallrich/timesaveR')
install_github("oliviasabik/RACER") 
install_github("dzhang32/ggtranscript")
install_github("openanalytics/gread")