Computational Biology Course (St. Jude Graduate School)

Lecture 4: Tools for RNA-seq analysis and interpretation (Slides | Companion document)

Script for basic DESeq2 analysis: (UPLOAD KNITR FILE HERE)

Script for creating the prepared data below: (UPLOAD)

RNA-seq count data and TPM expression estimates for the above script: http://geeleherlab.org/teachingFiles/brcaHer2.RData

Expression data for GSEA: http://geeleherlab.org/teachingFiles/her2Expr.gct

Phenotype data for GSEA: http://geeleherlab.org/teachingFiles/her2Labels.cls

Gene symbols “.chip” file for GSEA: http://geeleherlab.org/teachingFiles/GENE_SYMBOL.chip