SCMBench/environments/env4_R_install.r at main · ml4bio/SCMBench · GitHub

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# package library and install
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager", repos = "http://cran.us.r-project.org")
if (!requireNamespace("EnsDb.Hsapiens.v86", quietly = TRUE))
  BiocManager::install("EnsDb.Hsapiens.v86")
if (!requireNamespace("EnsDb.Mmusculus.v79", quietly = TRUE))
  BiocManager::install("EnsDb.Mmusculus.v79")
if (!requireNamespace("scater", quietly = TRUE))
  BiocManager::install("scater")
if (!requireNamespace("bluster", quietly = TRUE))
  BiocManager::install("bluster")
if (!requireNamespace("GenomeInfoDb", quietly = TRUE))
  BiocManager::install("GenomeInfoDb")
if (!requireNamespace("GenomeInfoDb", quietly = TRUE))
  BiocManager::install("GenomeInfoDb")
if (!requireNamespace("IRanges", quietly = TRUE))
  BiocManager::install("IRanges")
if (!requireNamespace("ComplexHeatmap", quietly = TRUE))
  BiocManager::install("ComplexHeatmap")
if (!requireNamespace("rtracklayer", quietly = TRUE))
  BiocManager::install ("rtracklayer")
if (!requireNamespace("devtools", quietly = TRUE))
  install.packages("devtools")
if (!requireNamespace("RColorBrewer", quietly = TRUE))
  install.packages('RColorBrewer')
if (!requireNamespace("reticulate", quietly = TRUE))
  install.packages("reticulate")
if (!requireNamespace("plyr", quietly = TRUE))
  install.packages('plyr')
if (!requireNamespace("dsb", quietly = TRUE))
  install.packages('dsb')
if (!requireNamespace("Seurat", quietly = TRUE))
  install.packages('Seurat')
if (!requireNamespace("Signac", quietly = TRUE))
  install.packages("Signac")
if (!requireNamespace("cluster", quietly = TRUE))
  install.packages("cluster")
if (!requireNamespace("igraph", quietly = TRUE))
  install.packages ("igraph")
if (!requireNamespace("ggplot2", quietly = TRUE))
  install.packages ("ggplot2")
if (!requireNamespace("Matrix", quietly = TRUE))
  install.packages ("Matrix")
if (!requireNamespace("dplyr", quietly = TRUE))
  install.packages("dplyr")
if (!requireNamespace("tinytex", quietly = TRUE))
  install.packages("tinytex")
if (!requireNamespace("tidyverse", quietly = TRUE))
  install.packages ( "tidyverse" )
if (requireNamespace("devtools", quietly = TRUE))
  library(devtools)
if (!requireNamespace("MAESTRO", quietly = TRUE))
  install_github("liulab-dfci/MAESTRO")
if (!requireNamespace("data.table", quietly = TRUE))
  install.packages("data.table")
if (!requireNamespace("igraph", quietly = TRUE))
  install.packages ("igraph")
if (!requireNamespace("parallel", quietly = TRUE))
  install.packages("parallel")
if (!requireNamespace("dplyr", quietly = TRUE))
  install.packages("dplyr")
if (!requireNamespace("Hmisc", quietly = TRUE))
  install.packages("Hmisc")
if (!requireNamespace("CellChat", quietly = TRUE))
  devtools::install_github("sqjin/CellChat")
if (!requireNamespace("patchwork", quietly = TRUE))
  devtools::install_github("thomasp85/patchwork")
if (!requireNamespace("RcppPlanc", quietly = TRUE))
  install.packages("RcppPlanc", repos = c(linux = 'https://welch-lab.r-universe.dev/bin/linux/noble/4.4/',
  sources = 'https://welch-lab.r-universe.dev',
  cran = 'https://cloud.r-project.org'))
if (!requireNamespace("rliger", quietly = TRUE))
  install.packages("rliger")