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install_uengs.R

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  • Carine's avatar
    Carine Rey authored
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    install_uengs.R 1.08 KiB
    options(Ncpus = parallel::detectCores())
    options(repos = c(CRAN = "https://cran.rstudio.com"))
    
    # Installation of standard R packages
    install.packages(c("remotes",
                       "Seurat",
                       "mvoutlier",
                       "preseqR"))
    
    # Installation of packages with BiocManager
    install.packages("BiocManager")
    BiocManager::install(
        c("biomaRt",
          "clusterProfiler",
          "apeglm",
          "scater",
          "rhdf5",
          "idr"
        ), ask = FALSE)
    
    
    BiocManager::install(c("eisaR",
                           "BSgenome",
                           "fishpond",
                           "GenomicFeatures"))
    install.packages("devtools")
    
    devtools::install_github("COMBINE-lab/roe")
    
    # Install R package from GitHub
    #remotes::install_github("satijalab/seurat-data", "seurat5", quiet = TRUE)
    #remotes::install_github("satijalab/azimuth", "seurat5", quiet = TRUE)
    #remotes::install_github("satijalab/seurat-wrappers", "seurat5", quiet = TRUE)
    
    #Serat Wrapper
    install.packages(c("hwriter",
                       "RcppParallel",
                       "latticeExtra"))
    
    BiocManager::install("dada2")