Intermediate R / Bioconductor for High-Throughput Sequence Analysis

Seattle, USA

2013-05-28 ~ 2013-05-29

Instructors

Description

Intermediate R / Bioconductor for High-Throughput Sequence Analysis introduces users with some R experience to common Bioconductor work flows for sequence analysis. The course involves a combination of presentations and hands-on exercises. Our starting point is BAM files created by aligning short reads to a reference genome. Topics include exploratory analysis (GenomicRanges, Rsamtools); assessing differential expression of known genes (DESeq); detection, calling, and manipulation of variants (VariantTools, VariantAnnotation). We learn how to integrate results with curated gene and genomic annotations (GenomicFeatures), and to visualize results (GViz, ggbio).

Materials

IntermediateSequenceAnalysis2013 Package:

R Script PDF

Users of R 3.0 / Bioconductor 2.12 can install the package with

source("http://bioconductor.org/scratch-repos/pkgInstall.R")
pkgInstall("IntermediateSequenceAnalysis2013")

Bioconductor Release »

Packages in the stable, semi-annual release:


Bioconductor is also available as an Amazon Machine Image.
Fred Hutchinson Cancer Research Center