2011-10-17 ~ 2011-10-18
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.
|9-11||Introduction to R and Bioconductor|
|11-12, 1-2||Working with sequences, ranges and annotations|
|9-11:15||RNA-seq differential representation|
|11:15-12, 1-2:30||Approaches to ChIP-seq|
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"))
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
Bioconductor Release »
Packages in the stable, semi-annual release:
Common Bioconductor workflows include: