- Home
- Help
- Courses and Conferences
- 2011
- Introduction to R/Bioconductor for Sequence Analysis
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 | |
9-11 | Introduction to R and Bioconductor |
11-12, 1-2 | Working with sequences, ranges and annotations |
2-4 | Exploring sequences |
Tuesday | |
9-11:15 | RNA-seq differential representation |
11:15-12, 1-2:30 | Approaches to ChIP-seq |
2:30-4 | Gene-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