Introduction to R and Bioconductor

Seattle, USA

2010-01-27 ~ 2010-01-29

Instructors

• Chao-Jen Wong
• Herve Pages
• Marc Carlson
• Martin Morgan
• Nishant Gopalakrishnan
• Patrick Aboyoun
• Seth Falcon

Description

This course introduces R and Bioconductor tools for analysis of high-throughput microarray and short read sequence data. It is designed for beginning or intermediate users of R and Bioconductor. A major theme for this workshop is reproducible research. To that end, participants will develop their own R package containing work developed during the course.

Materials

• Day 1: R Package (day1_0.0.1.tar.gz)
  • First Steps with R
  • First Steps with R (solutions)
  • Getting Started with Lattice
  • Basic Lattice (solutions)
  • Building an R Package
  • Building an R Package (solutions)
  • ALL Dataset
• Day 2: R Package (day2_0.0.11.tar.gz)
  • Pre-processing
  • Pre-processing Lab
  • Pre-processing Lab (solutions)
  • Differential Expression
  • Differential Expression (solutions)
  • Gene Set Enrichment Analysis
  • Bioconductor Annotation Packages
• Day 3: R Package (day3_0.0.3.tar.gz)
  • String Basics
  • String Basics (solutions)
  • High throughput sequence I/O, manipulation, and quality assessment
  • ShortRead Lab: Working with Aligned Sequences
  • ShortRead Lab: Working with Aligned Sequences (solutions)
  • Exploratory Data Analysis of Coverage
  • Sequence Annotation
  • Finding RNA-seq Hot Spots
  • Simple RNA-seq Expression Measures
  • ChIP-seq peak identification and analysis