Course package vignette:

PDF | R

Course package:

This package is already installed on your AMI. But you can install it on your own machine as follows:

useR2013_0.1.5.tar.gz

Download the file above and install as follows in R-3.0, starting R in the directory where you downloaded the file:

biocLite(c("GenomicFeatures", "ShortRead", "VariantAnnotation",
  "edgeR", "bioDist", "DiffBind", "org.Dm.eg.db",
  "BSgenome.Dmelanogaster.UCSC.dm3",
  "TxDb.Dmelanogaster.UCSC.dm3.ensGene",
  "BSgenome.Hsapiens.UCSC.hg19",
  "TxDb.Hsapiens.UCSC.hg19.knownGene",
  "SNPlocs.Hsapiens.dbSNP.20101109", "MotifDb", "seqLogo",
  "ggplot2"))
install.packages("useR2013_0.1.5.tar.gz", repos=NULL, type="source")