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- Intermediate R / Bioconductor for High-Throughput Sequence Analysis
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:
Users of R 3.0 / Bioconductor 2.12 can install the package with
source("http://bioconductor.org/scratch-repos/pkgInstall.R")
pkgInstall("IntermediateSequenceAnalysis2013")