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.