Tutorials

Introduction to R

The tutorial is presented as a set of slides with the expectation that the reader will follow along typing the commands into R. The materials for the tutorial are: In this tutorial, I give an overview of basic R concepts including:

Accomplishing Exome Sequencing Data Tasks with Bioconductor

This tutorial gives a few examples of how R and Bioconductor can be used to examine exome sequencing data. The pdf version of the tutorial is here. To get started, paste the following code into an R session. The BasicExomeExample package should be installed, also.

# install the BasicExomeExample package
install.packages('BasicExomeExample',
  contriburl=contrib.url('http://watson.nci.nih.gov/~sdavis/software/R',
  type='source'),type='source')
# these are the vignette code examples, Sweave document, and PDF
download.file('http://watson.nci.nih.gov/~sdavis/BiocExomeData.R',
  'BiocExomeData.R')
download.file('http://watson.nci.nih.gov/~sdavis/BiocExomeData.Rnw',
  'BiocExomeData.Rnw')
browseURL('http://watson.nci.nih.gov/~sdavis/BiocExomeData.pdf')

A Simple Data Integration Exercise Using Data from the TCGA Project

This tutorial is a simplistic introduction to data integration through experience and utilizes R and Bioconductor tools. Data from 45 TCGA glioblastoma multiforme patients are used to demonstrate how even a relatively simple analysis can lead to very interesting biological hypotheses. The tutorial combines:

Accessing Public Data using R and Bioconductor

This little tutorial describes the tools used to access public data from the NCBI Gene Expression Omnibus (GEO) and the Sequence Read Archive (SRA). Tools covered include GEOquery, GEOmetadb, and SRAdb. A short section on using the Integrative Genomic Viewer (IGV) from the Broad institute to visualize aligned reads is also included.

The goals of this tutorial are to:

Introduction to Next-Generation Sequence Data Analysis Using Biowulf

The goals of this tutorial are to:

Although this tutorial is designed for use on the NIH Biowulf cluster, the tutorial is general enough that any linux or even Mac OS system can probably be used to good effect. Go to the tutorial or go to the talk.

Cold Spring Harbor 2010 Course Materials

The goals of this tutorial are to:

HTML version or PDF version of course materials.