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Intermediate R / Bioconductor for High-Throughput Sequence Analysis

Seattle, USA

2013-05-28 ~ 2013-05-29

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

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")