High throughput sequence analysis with R and Bioconductor

Warwick, UK

2011-08-16 ~ 2011-08-16

Instructors

Martin Morgan
Herve Pages

Description

This tutorial introduces R users to the Bioconductor project, a collection of more than 400 packages for the analysis and comprehension of high-throughput genetic data. The tutorial highlights flexible facilities for the analysis of DNA sequence data.

Materials

Welcome!

To prepare for this workshop, please install R version 2.13.1.

Exercises require additional packages. Install these by starting an R session and entering (e.g., cut-and-paste from below)

source("http://bioconductor.org/biocLite.R")
biocLite(c("GenomicFeatures", "ShortRead", "edgeR",
           "org.Dm.eg.db", "BSgenome.Dmelanogaster.UCSC.dm3"))

The workshop uses moderately sized data; your laptop (Mac, Windows, or Linux) should have 2 Gb or more of memory and ample disk space.
If using Linux or MacOS, download the Source package and install with
```
install.packages("useR2011_0.1.0.tar.gz", repos=NULL,
    type="source")
```
On windows, download the Windows package and install with
```
install.packages("useR2011_0.1.0.tar.gz", repos=NULL)
```
In either case, the first argument should be the path to the file that you downloaded!
Once installed, load the library and read the extensive vignette
```
library(useR2011)
browseVignettes("useR2011")
```
the package contains an extensive vignette (PDF) and R scripts for each chapter.

If you have questions, please do not hesitate to contact me, mtmorgan at fhcrc dot org.