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install_cran.R
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# CRAN packages
install.packages("devtools")
install.packages("pkgbuild")
library(devtools)
library(pkgbuild)
# Basic packages
devtools::install_version("commonmark", version = "1.9.1", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("xfun", version = "0.43", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("markdown", version = "1.12", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("rmarkdown", version = "2.26", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("tidyverse", version = "2.0.0", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("reticulate", version = "1.35.0", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("reshape2", version = "1.4.4", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("Matrix.utils", version = "0.9.8", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE) #removed from cran
devtools::install_version("Matrix", version = "1.6-5", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("data.table", version = "1.15.4", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("readr", version = "2.1.5", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("R.utils", version = "2.12.3", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("useful", version = "1.2.6.1", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("Rmisc", version = "1.5.1", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("stringdist", version = "0.9.12", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("janitor", version = "2.2.0", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("xlsx", version = "0.6.5", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("openxlsx2", version = "1.5", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("easyPubMed", version = "2.13", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
# visualization
devtools::install_version("RColorBrewer", version = "1.1-3", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("pheatmap", version = "1.0.12", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE) # not updated since 2019
devtools::install_version("ggrepel", version = "0.9.5", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("ggthemes", version = "5.1.0", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("ggnewscale", version = "0.4.10", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force=TRUE)
devtools::install_version("gplots", version = "3.1.3.1", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("ggbeeswarm", version = "0.7.2", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE) # not updated since 2017
devtools::install_version("ggsignif", version = "0.6.4", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("ggpubr", version = "0.6.0", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("ggVennDiagram", version = "1.5.2", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("ggExtra", version = "0.10.1", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("ggsci", version = "3.0.3", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("UpSetR", version = "1.4.0", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("aplot", version = "0.2.2", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("alluvial", version = "0.1-2", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("ggalluvial", version = "0.12.5", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("circlize", version = "0.4.16", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("viridis", version = "0.6.5", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("magick", version = "2.8.3", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("factoextra", version = "1.0.7", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("gridExtra", version = "2.3", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("multipanelfigure", version = "2.1.6", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("patchwork", version = "1.2.0", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
# statistics
devtools::install_version("corrplot", version = "0.92", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("dunn.test", version = "1.3.5", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("DirichletReg", version = "0.7-1", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("multcomp", version = "1.4-25", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
# Bioinformatics packages
devtools::install_version("Seurat", version = "5.0.3", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("tidyseurat", version = "0.8.0", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("SoupX", version = "1.6.2", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("igraph", version = "2.0.3", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("rliger", version = "2.0.0", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("harmony", version = "1.2.0", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("symphony", version = "0.1.1", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("doRNG", version = "1.8.6", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("sleepwalk", version = "0.3.2", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("tidydr", version = "0.0.5", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("dsb", version = "1.0.3", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("clustree", version = "0.5.1", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("scCustomize", version = "2.1.2", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)
devtools::install_version("seqinr", version = "4.2-36", repos = c("https://cran.uni-muenster.de/", "https://bioconductor.org/packages/3.18/bioc"), upgrade = "never", force = TRUE)