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 hgssmcgill@gmail.com 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).

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