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Introduction to R/Bioconductor for Sequence Analysis

Seattle, USA

2011-10-17 ~ 2011-10-18

Instructors

  • Martin Morgan
  • Hervé Pagès
  • Marc Carlson
  • Valerie Obenchain
  • Dan Tenenbaum

Description

This course introduces participants to the use of R and Bioconductor for the analysis of high throughput sequence data. Participants are expected to have basic familiarity with R, and with relevant biological domains. Participants can expect to gain a better understanding of how R works, and of the ways in which Bioconductor represents and manipulates sequence data. Participants will gain experience in simple work flows for the analysis of common next-generation sequence experiments.

Materials

Provisional agenda
Monday
9-11Introduction to R and Bioconductor
11-12, 1-2Working with sequences, ranges and annotations
2-4Exploring sequences
Tuesday
9-11:15RNA-seq differential representation
11:15-12, 1-2:30Approaches to ChIP-seq
2:30-4Gene-centric annotation

Course Vignette (PDF)

Annotation Slides (PDF)

Installing the course package on your computer

We will use R version 2.14 alpha. To install this version of R, visit (Windows, Mac OS, install from source or binary for Linux).
The course uses additional R and Bioconductor packages. To install these packages, start R and copy and paste the following command into your R session:

source("http://bioconductor.org/scratch-repos/pkgInstall.R")
pkgInstall(c("SeattleIntro2011", "SeattleIntro2011Data"))
Installing R from Source on Ubuntu Linux
sudo apt-get update
sudo apt-get install -y make libc6-dev gfortran gfortran-4.3 build-essential \
  libreadline5-dev libx11-dev libxt-dev libcurl4-openssl-dev libxml2-dev \
  texlive-full tcl8.5-dev tk8.5-dev libxss-dev libpng12-dev libjpeg62-dev \
  libcairo2-dev gcj
curl -O http://cran.fhcrc.org/src/base-prerelease/R-latest.tar.gz
tar zxf R-latest.tar.gz
cd R-alpha # or R-beta if this does not work
./configure
make
sudo make install