Introduction to R/Bioconductor for Sequence Analysis

Seattle, USA

2011-10-17 ~ 2011-10-18

Instructors

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
## [Course Vignette (PDF)](Bioconductor-tutorial.pdf) ## [Annotation Slides (PDF)](AnnotationSlides.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
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

Packages »

Bioconductor's stable, semi-annual release:

Bioconductor is also available via Docker and Amazon Machine Images.

Documentation »

Bioconductor

R / CRAN packages and documentation

Fred Hutchinson Cancer Research Center