Advanced R Workshop

Edit: The slides and code are now available in the Shared Google Drive or GitHub.

The Advanced R Workshop will take place on Tuesday March 28th from 9am to 5pm in room N4/17 (Stewart Bio). Lunch is not provided but we will provide snacks and coffee.

You can register by emailing us at by Friday March 24th.

This workshop will show ways to analyze and visualize large genomics data. Here is a plan of the content:

  • Optimizing your code.
    • Reading/analyzing large files.
      • Tips to read files faster.
      • Chunk-by-chunk approach.
      • Reading genomics formats with Bioconductor packages (vcf, gff, gtf, bam).
      • Using file indexing in R (e.g. tabix, vcf, bam).
    • Overview of dplyr for data manipulation.
    • Avoiding “for” loops.
    • Parallelization (multi-processor and on computing clusters).
  • Manipulating genomics intervals.
  • Visualization.
    • Gviz to produce multi-tracks graph of a particular region.
    • dplyr + ggplot2 to quickly explore global patterns.
  • Automated reports with RMarkdown: quick overview and tips for a smooth compilation.

Caution: Participants will be expected to know R basics (read/write files, manipulate data.frames, write functions).