Notes for PM2: Working with Bioconductor Tools for High-Throughput Sequencing Data: ShortRead, GenomeGraphs, and IRanges

The short course on R/Bioconductor tools for the analysis of next generation sequencing data will require a number of R packages and tools in order to fully perform all of the examples. These tools are all freely available and readily installable on all the major platforms.

1. R 2.9.1 (The current release version of R)
   http://cran.r-project.org/


2. The Bioconductor packages (http://bioconductor.org):
   ShortRead, Biostrings, IRanges, GenomeGraphs, biomaRt
   
   These are most easily installed, by launching R and then executing the following code:
   
   R> source("http://bioconductor.org/biocLite.R")
   R> biocLite(c("ShortRead", "GenomeGraphs"))
   
   This should install the necessary dependencies as well.


3. Bowtie, available at:
   http://bowtie-bio.sourceforge.net/
   
   You should download the most recent version: 0.10.1. Additionally, you should download the S. cerevisiae, CYGD index.

I will have all of these packages availabe for install at the course and we'll try to get everyone a working environmnent for the tutorial.