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Intermediate R / Bioconductor for High-Throughput Sequence Analysis

Seattle, USA

2013-02-14 ~ 2013-02-15

Instructors

  • Martin Morgan
  • Hervé Pagès
  • Marc Carlson
  • Valerie Obenchain
  • Dan Tenenbaum
  • Paul Shannon

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

Course Vignette

The vignette is useful to all. Users of R 3.0 / Bioconductor 2.12 can install the package with

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