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install_R_packages.R
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options(repos = BiocManager::repositories())
if (!require("devtools")) install.packages("devtools", repos="http://cran.us.r-project.org")
if (!require("shiny")) install.packages("shiny", repos="http://cran.us.r-project.org")
if (!require("shinythemes")) install.packages("shinythemes", repos="http://cran.us.r-project.org")
if (!require("tidyverse")) install.packages("tidyverse", repos="http://cran.us.r-project.org")
if (!require("stringr")) install.packages("stringr", repos="http://cran.us.r-project.org")
if (!require("servr")) install.packages("servr", repos="http://cran.us.r-project.org")
if (!require("ggplot2")) install.packages("ggplot2", repos="http://cran.us.r-project.org")
if (!require("pheatmap")) install.packages("pheatmap", repos="http://cran.us.r-project.org")
if (!require("heatmaply")) install.packages("heatmaply", repos="http://cran.us.r-project.org")
if (!require("plotly")) install.packages("plotly", repos="http://cran.us.r-project.org")
if (!require("shinyjs")) install.packages("shinyjs", repos="http://cran.us.r-project.org")
if (!require("shinyBS")) install.packages("shinyBS", repos="http://cran.us.r-project.org")
if (!require("msigdbr")) install.packages("msigdbr", repos="http://cran.us.r-project.org")
if (!require("fontawesome")) install.packages("fontawesome", repos="http://cran.us.r-project.org")
if (!require("shinycssloaders")) install.packages("shinycssloaders", repos="http://cran.us.r-project.org")
if (!require("DT")) install.packages("DT", repos="http://cran.us.r-project.org")
if (!require("e1071")) install.packages("e1071", repos="http://cran.us.r-project.org")
if (!require("dplyr")) install.packages("dplyr", repos="http://cran.us.r-project.org")
if (!require("pbmcapply")) install.packages("pbmcapply", repos="http://cran.us.r-project.org")
if (!require("reshape2")) install.packages("reshape2", repos="http://cran.us.r-project.org")
if (!require("shinydashboard")) install.packages("shinydashboard", repos="http://cran.us.r-project.org")
if (!require("shinyalert")) install.packages("shinyalert", repos="http://cran.us.r-project.org")
if (!require("shinyFiles")) install.packages("shinyFiles", repos="http://cran.us.r-project.org")
if (!require("igraph")) install.packages("igraph", repos="http://cran.us.r-project.org")
if (!require("cluster")) install.packages("cluster", repos="http://cran.us.r-project.org")
if (!require("RANN")) install.packages("RANN", repos="http://cran.us.r-project.org")
if (!require("shinyWidgets")) install.packages("shinyWidgets", repos="http://cran.us.r-project.org")
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
if (!require("scales")) install.packages("scales", repos="http://cran.us.r-project.org")
if (!require("dtwclust")) install.packages("dtwclust", repos="http://cran.us.r-project.org")
if (!require("anndata")) install.packages("anndata", repos="http://cran.us.r-project.org")
if (!require("reticulate")) install.packages("reticulate", repos="http://cran.us.r-project.org")
if (!require("tibble")) install.packages("tibble", repos="http://cran.us.r-project.org")
if (!require("clustree")) install.packages("clustree", repos="http://cran.us.r-project.org")
if (!require("magrittr")) install.packages("magrittr", repos="http://cran.us.r-project.org")
if (!require("cowplot")) install.packages("cowplot", repos="http://cran.us.r-project.org")
if (!require("rhandsontable")) install.packages("rhandsontable", repos="http://cran.us.r-project.org")
if (!require("sctransform")) install.packages("sctransform", repos="http://cran.us.r-project.org")
if (!require("data.table")) install.packages("data.table", repos="http://cran.us.r-project.org")
if (!require("purrr")) install.packages("purrr", repos="http://cran.us.r-project.org")
if (!require("scater")) BiocManager::install("scater", update = FALSE)
if (!require("fgsea")) BiocManager::install("fgsea", update = FALSE)
if (!require("MOFA2")) BiocManager::install("MOFA2", update = FALSE)
if (!require("EnhancedVolcano")) BiocManager::install("EnhancedVolcano", update = FALSE)
if (!require("liana")) remotes::install_github('saezlab/liana')
if (!require("rGREAT")) install_github("jokergoo/rGREAT")
if (!require("biovizBase")) BiocManager::install("biovizBase", update = FALSE)
if (!require("GenomeInfoDb")) BiocManager::install("GenomeInfoDb", update = FALSE)
if (!require("BSgenome.Hsapiens.UCSC.hg19")) BiocManager::install("BSgenome.Hsapiens.UCSC.hg19", update = FALSE)
#if (!require("cytomapper")) BiocManager::install("cytomapper", update = FALSE)
#if (!require("FlowSOM")) BiocManager::install("FlowSOM", update = FALSE)
#if (!require("cytofkit2")) devtools::install_github("JinmiaoChenLab/cytofkit2", dependencies=TRUE)
if (!require("lisi")) devtools::install_github("immunogenomics/lisi", dependencies=TRUE)
if (!require("ktplots")) devtools::install_github('zktuong/ktplots', dependencies = TRUE)
if (!require("EnsDb.Hsapiens.v86")) BiocManager::install("EnsDb.Hsapiens.v86", update = FALSE)
#if (!require("flowCore")) BiocManager::install("flowCore", update = FALSE)
if (!require("harmony")) BiocManager::install("harmony")
#if (!require("rliger")) install.packages('rliger')
if (!require("cowplot")) install.packages('cowplot')
#if (!require("Rphenograph")) devtools::install_github("JinmiaoChenLab/Rphenograph", upgrade=TRUE)
#if (!require("CellChat")) devtools::install_github("sqjin/CellChat", upgrade=TRUE)
if (!require("sceasy")) devtools::install_github("cellgeni/sceasy", upgrade=TRUE)
if (!require("leidenbase")) devtools::install_github('cole-trapnell-lab/leidenbase')
#if (!require("monocle3")) devtools::install_github('cole-trapnell-lab/monocle3')
#if (!require("SPOTlight")) devtools::install_github("https://github.com/MarcElosua/SPOTlight", upgrade=TRUE)
if (!require("FastIntegration")) devtools::install_github("[email protected]:JinmiaoChenLab/FastIntegrate.git", upgrade=TRUE)
if (!require("hdf5r")) install.packages("hdf5r", repos="http://cran.us.r-project.org")
if (!require("Seurat")) install.packages("Seurat", repos="http://cran.us.r-project.org")
if (!require("bslib")) install.packages("bslib", repos="http://cran.us.r-project.org")
if (!require("shinyWidgets")) install.packages("shinyWidgets")
if (!require("SeuratWrappers")) remotes::install_github('satijalab/seurat-wrappers')
if (!require("Signac")) install.packages("Signac", repos="http://cran.us.r-project.org")