source("http://bioconductor.org/biocLite.R") courseRepos <- "http://bioconductor.org/course-packages" allRepos <- c(courseRepos, biocinstallRepos()) allPkgs <- c("HTSandGeneCentricLabs", "IRanges", "GenomicRanges", "Biostrings", "BSgenome", "rtracklayer", "biomaRt", "GenomicFeatures", "Rsamtools", "ShortRead", "EatonEtAlChIPseq", "leeBamViews", "RSQLite", "GO.db", "KEGG.db", "RCurl", "org.Sc.sgd.db", "yeast2.db", "yeast2probe", "ygs98probe", "BSgenome.Scerevisiae.UCSC.sacCer2", "org.Hs.eg.db", "hgu95av2.db") update.packages(repos = allRepos, ask = FALSE) newPkgs <- setdiff(allPkgs, installed.packages()) if (length(newPkgs) > 0) install.packages(newPkgs, repos = allRepos)