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install_packages.R
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# Functions
install.cran <- function(package, version, host="cloud.r-project.org"){
install.packages(paste0("https://",host,"/src/contrib/Archive/",package,"/",package,"_",version,".tar.gz"), repos = NULL)
}
install.bioconductor <- function(package, version, bioconductor_version, source = "bioc"){
install.packages(paste0("https://www.bioconductor.org/packages/",bioconductor_version,"/",source,"/src/contrib/",package,"_",version,".tar.gz"), repos = NULL)
}
# CRAN packages
install.cran("rlang", version="0.1.1")
install.cran("Rcpp", version="0.12.11")
install.cran("RcppArmadillo", version="0.7.900.2.0")
install.cran("bitops", version="1.0-6")
install.cran("RCurl", version="1.95-4.8")
install.cran("Rtsne", version="0.13")
install.cran("MASS", version="7.3-47")
install.cran("RColorBrewer", version="1.1-2")
install.cran("colorspace", version="1.3-2")
install.cran("munsell", version="0.4.3")
install.cran("gtable", version="0.2.0")
install.cran("digest", version="0.6.12")
install.cran("memoise", version="1.1.0")
install.cran("htmltools", version="0.3.6")
install.cran("pkgconfig", version="2.0.1")
install.cran("magrittr", version="1.5")
install.cran("lazyeval", version="0.2.0")
install.cran("tibble", version="1.3.3")
install.cran("stringi", version="1.1.5")
install.cran("stringr", version="1.2.0")
install.cran("glue", version="1.1.1")
install.cran("plyr", version="1.8.4")
install.cran("reshape2", version="1.4.2")
install.cran("assertthat", version="0.2.0")
install.cran("bindr", version="0.1")
install.cran("R6", version="2.2.2")
install.cran("plogr", version="0.1-1")
install.cran("bindrcpp", version="0.2")
install.cran("BH", version="1.62.0-1")
install.cran("dichromat", version="2.0-0")
install.cran("labeling", version="0.3")
install.cran("scales", version="0.4.1")
install.cran("pheatmap", version="1.0.8")
install.cran("ggplot2", version="2.2.1")
install.cran("gridExtra", version="2.2.1")
install.cran("viridisLite", version="0.2.0")
install.cran("viridis", version="0.4.0")
install.cran("RJSONIO", version="1.3-1.2")
install.cran("jsonlite", version="1.6")
install.cran("yaml", version="2.1.14")
install.cran("htmlwidgets", version="0.8")
install.cran("png", version="0.1-7")
install.cran("base64enc", version="0.1-3")
install.cran("modeltools", version="0.2-21")
install.cran("flexmix", version="2.3-13")
install.cran("mvtnorm", version="1.0-6")
install.cran("DEoptimR", version="1.0-8")
install.cran("robustbase", version="0.92-7")
install.cran("mgcv", version="1.8-23")
install.cran("nlme", version="3.1-131.1")
install.cran("iterators", version="1.0.8")
install.cran("foreach", version="1.4.3")
install.cran("lattice", version="0.20-35")
install.cran("matrixStats", version="0.52.2")
install.cran("irlba", version="2.2.1")
install.cran("igraph", version="1.1.1")
install.cran("networkD3", version="0.4")
install.cran("cluster", version="2.0.6")
install.cran("data.table", version="1.10.4")
install.cran("backports", version="1.1.0")
install.cran("Formula", version="1.2-1")
install.cran("latticeExtra", version="0.6-28")
install.cran("acepack", version="1.4.1")
install.cran("checkmate", version="1.8.3")
install.cran("evaluate", version="0.10.1")
install.cran("highr", version="0.6")
install.cran("mime", version="0.5")
install.cran("markdown", version="0.8")
install.cran("knitr", version="1.16")
install.cran("htmlTable", version="1.9")
install.cran("Hmisc", version="4.0-3")
install.cran("httpuv", version="1.3.5")
install.cran("xtable", version="1.8-2")
install.cran("sourcetools", version="0.1.6")
install.cran("shiny", version="1.0.3")
install.cran("shinydashboard", version="0.6.1")
install.cran("gtools", version="3.5.0")
install.cran("gdata", version="2.18.0")
install.cran("RMTstat", version="0.3")
install.cran("doParallel", version="1.0.10")
install.cran("caTools", version="1.17.1")
install.cran("gplots", version="3.0.1")
install.cran("ROCR", version="1.0-7")
install.cran("blob", version="1.1.0")
install.cran("WriteXLS", version="4.0.0")
install.cran("brew", version="1.0-6")
install.cran("survival", version="2.41-3")
install.cran("registry", version="0.3")
install.cran("MatrixModels", version="0.4-1")
install.cran("Rook", version="1.1-1")
install.cran("SparseM", version="1.77")
install.cran("DBI", version="0.7")
install.cran("pkgmaker", version="0.22")
install.cran("rngtools", version="1.2.4")
install.cran("foreign", version="0.8-69")
install.cran("bit", version="1.1-12")
install.cran("ff", version="2.2-13")
install.cran("distillery", version="1.0-4")
install.cran("XML", version="3.98-1.9")
install.cran("nnet", version="7.3-12")
install.cran("locfit", version="1.5-9.1")
install.cran("bit64", version="0.9-7")
install.cran("RSQLite", version="2.0")
install.cran("doRNG", version="1.6.6")
install.cran("quantreg", version="5.33")
install.cran("beeswarm", version="0.2.3")
install.cran("e1071", version="1.6-8")
install.cran("statmod", version="1.4.30")
install.cran("pcaPP", version="1.9-72")
install.cran("Matrix", version="1.2-10")
install.cran("nloptr", version="1.0.4")
install.cran("minqa", version="1.2.4")
install.cran("RcppEigen", version="0.3.3.3.0")
install.cran("lme4", version="1.1-13")
install.cran("pbkrtest", version="0.4-7")
install.cran("car", version="2.1-5")
install.cran("Lmoments", version="1.2-3")
install.cran("extRemes", version="2.0-8")
install.cran("rrcov", version="1.4-3")
install.cran("KernSmooth", version="2.23-15")
install.cran("vipor", version="0.4.5")
install.cran("codetools", version="0.2-15")
install.cran("rjson", version="0.2.15")
install.cran("rpart", version="4.1-11")
install.cran("class", version="7.3-14")
install.cran("Cairo", version="1.5-9")
install.cran("ggbeeswarm", version="0.5.3")
install.cran("mclust", version="5.3")
install.cran("prabclus", version="2.2-6")
install.cran("diptest", version="0.75-7")
install.cran("kernlab", version="0.9-25")
install.cran("trimcluster", version="0.1-2")
install.cran("fpc", version="2.1-10")
install.cran("whisker", version="0.3-2")
install.cran("dendextend", version="1.5.2")
install.cran("d3heatmap", version="0.6.1.1")
install.cran("curl", version="2.7")
install.cran("openssl", version="0.9.6")
install.cran("httr", version="1.2.1")
install.cran("dplyr", version="0.7.1")
install.cran("getopt", version="1.20.0")
install.cran("ggrepel", version="0.7.0")
install.cran("heatmap.plus", version="1.3")
install.cran("rstudioapi", version="0.6")
install.cran("git2r", version="0.18.0")
install.cran("withr", version="1.0.2")
install.cran("devtools", version="1.13.2")
install.cran("fastICA", version="1.2-1")
install.cran("combinat", version="0.0-8")
install.cran("slam", version="0.1-42")
install.cran("qlcMatrix", version="0.9.5")
install.cran("RUnit", version="0.4.31")
install.cran("permute", version="0.9-4")
install.cran("vegan", version="2.4-3")
install.cran("gridBase", version="0.4-7")
install.cran("sp", version="1.2-5")
install.cran("maps", version="3.2.0")
install.cran("shapefiles", version="0.7")
install.cran("fossil", version="0.3.7")
install.cran("ellipse", version="0.3-8")
install.cran("scatterplot3d", version="0.3-40")
install.cran("flashClust", version="1.01-2")
install.cran("leaps", version="3.0")
install.cran("FactoMineR", version="1.36")
install.cran("VGAM", version="1.0-5")
install.cran("FNN", version="1.1")
install.cran("densityClust", version="0.3")
install.cran("NMF", version="0.20.6")
install.cran("proxy", version="0.4-22")
install.cran("SNFtool", version="2.2.1")
install.cran("RANN", version="2.5.1")
install.cran("optparse", version="1.4.4")
install.cran("ineq", version="0.2-13")
install.cran("DDRTree", version="0.1.5")
install.cran("snow", version="0.4-2")
install.cran("futile.options", version="1.0.0")
install.cran("lambda.r", version="1.1.9")
install.cran("futile.logger", version="1.4.3")
#Bioconductor packages
install.bioconductor("limma", version="3.32.10", "3.5") # Instead of 3.32.2
install.bioconductor("edgeR", version="3.18.1", "3.5")
install.bioconductor("BiocGenerics", version="0.24.0", "3.6")
install.bioconductor("Biobase", version="2.36.2", "3.5")
install.bioconductor("S4Vectors", version="0.16.0", "3.6")
install.bioconductor("BiocParallel", version="1.10.1", "3.5")
install.bioconductor("IRanges", version="2.12.0", "3.6")
install.bioconductor("zlibbioc", version="1.22.0", "3.5")
install.bioconductor("XVector", version="0.16.0", "3.5")
install.bioconductor("GenomeInfoDbData", version="0.99.0", "3.5", "data/annotation")
install.bioconductor("GenomeInfoDb", version="1.14.0", "3.6")
install.bioconductor("GenomicRanges", version="1.30.3", "3.6")
install.bioconductor("DelayedArray", version="0.4.1", "3.6")
install.bioconductor("SummarizedExperiment", version="1.8.1", "3.6")
install.bioconductor("AnnotationDbi", version="1.38.2", "3.5") # Instead of 1.38.1
install.bioconductor("annotate", version="1.54.0", "3.5")
install.bioconductor("genefilter", version="1.58.1", "3.5")
install.bioconductor("geneplotter", version="1.54.0", "3.5")
install.bioconductor("DESeq2", version="1.16.1", "3.5")
install.bioconductor("BiocInstaller", version="1.28.0", "3.6")
install.bioconductor("Biostrings", version="2.44.2", "3.5") # Instead of 2.44.1
install.bioconductor("sva", version="3.26.0", "3.6")
install.bioconductor("affyio", version="1.46.0", "3.5")
install.bioconductor("GEOquery", version="2.42.0", "3.5")
install.bioconductor("preprocessCore", version="1.38.1", "3.5")
install.bioconductor("affy", version="1.54.0", "3.5")
install.bioconductor("affxparser", version="1.48.0", "3.5")
install.bioconductor("oligoClasses", version="1.38.0", "3.5")
install.bioconductor("oligo", version="1.40.2", "3.5") # Instead of 1.40.1
install.bioconductor("pcaMethods", version="1.68.0", "3.5")
install.bioconductor("scde", version="2.6.0", "3.6") # Instead of 2.5.0
install.bioconductor("tximport", version="1.4.0", "3.5")
install.bioconductor("biomaRt", version="2.32.1", "3.5")
install.bioconductor("rhdf5", version="2.20.0", "3.5")
install.bioconductor("scater", version="1.4.0", "3.5")
install.bioconductor("SC3", version="1.4.2", "3.5")
install.bioconductor("SCAN.UPC", version="2.18.0", "3.5")
install.bioconductor("HSMMSingleCell", version="0.112.0", "3.6", "data/experiment")
install.bioconductor("graph", version="1.56.0", "3.6")
install.bioconductor("RBGL", version="1.54.0", "3.6")
install.bioconductor("biocViews", version="1.46.0", "3.6")
install.bioconductor("monocle", version="2.6.4", "3.6")
# FAILS
#install.cran("rPython", version="0.0-6")
#install.cran("scLVM", version="0.99.3")