Rafael Irizarry, author of rafalib, has put together a set of courses:

Text Docker image with all required packages: Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.1.

  • RNA-seq data analysis
    • exon-by-exon relative count as exon_i and all other exons for that gene;
    • cufflinks analysis at isoform(variant level) compare across tissue samples
    • FPKM read is lower >1 isoform/gene
  • Intro to Bioconductor
    • datasets: humangenome, snpdb
    • libraries: dplyr
  • StatsI/II

  • Linear Models/Matrices
    • lm
    • QR factorization
    • SVD
  • ChIP-seq data
  • DNA methylation
  • Variant Discovery and Genotyping