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DKFZ Fortbildung 2009

In November 2009 and February 2010 I held the Advanced R Programming Seminar in my working institute German Cancer Research Center. Another introductory workshop, Essential R and Bioconductor, was also given by me to the scientists and PhD students working at the DKFZ in January 2010. Two seminars share much presentation material. The R part is mainly created by myself, whereas many pages for the Bioconductor are borrowed from the package authors with permission. Many thanks to them! You can get the presentations (in PDF) by clicking the part titles.

The topics include:

Part 1: R as a programming language

  • Warm-up with R essentials
  • Debugging and Profiling tools
  • Object-oriented programming, S4-class and generic methods
  • Interfacing to C/C++ code
  • UNIT tests in R with RUnit
  • Efficient R-programming with ESS or StatET
  • Q&A

Part 2: Bioconductor project in R

  • Advanced graphics in R (lattice, Rgraphviz)
  • Bioconductor: writing packages and documentation
  • Microarray analysis: preprocessing, differential expression analysis and annotation
  • Gene Set Enrichment Analysis (GSEA)
  • API to bioinformatic resources, i.e. databases.
  • Infrastructure and framework for Next-Generation Sequencing (NGS) applications
  • Q&A