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install_dependencies.R 1.6 KiB
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Renato Alves's avatar
Add instructions and validate that all libraries loaded correctly
Renato Alves committed
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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"))"