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 across tissue samples
- FPKM read is lower >1 isoform/gene
- Intro to Bioconductor
- datasets: humangenome, snpdb
- libraries: dplyr
- Linear Models/Matrices
- lm
- QR factorization
- SVD
- ChIP-seq data
- DNA methylation
- Variant Discovery and Genotyping