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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.