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