Install packages for Thomas Carroll ATAC-seq NYC R/Bioconductor meet-up

installpkgs.R

mypkgs <- rownames(installed.packages())

if (!require("BiocInstaller")) {
  source("http://www.bioconductor.org/biocLite.R")
  biocLite(ask = FALSE)
}

if (!require("devtools"))
  biocLite("devtools", ask = FALSE)

requiredpkgs <- c(
  "Rsamtools",
  "GenomicAlignments",
  "TxDb.Hsapiens.UCSC.hg19.knownGene",
  "soGGi",
  "rtracklayer",
  "ChIPQC",
  "ChIPseeker",
  "rGREAT",
  "limma",
  "DESeq2",
  "TxDb.Mmusculus.UCSC.mm10.knownGene",
  "tracktables",
  "clusterProfiler",
  "org.Mm.eg.db",
  "MotifDb",
  "Biostrings",
  "BSgenome.Hsapiens.UCSC.hg19",
  "knitr",
  "rmdformats",
  "dplyr",
  "DT",
  "tidyr",
  "ggplot2",
  "magrittr",
  "devtools",
  "ThomasCarroll/soGGi"
)

biocLite(setdiff(requiredpkgs, mypkgs),  ask = FALSE)