R and bioinformatics

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 $\delta$ 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