2011-08-16 ~ 2011-08-16
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.
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
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
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.