Computational Biology Course (St. Jude Graduate School)
Lecture 4: Tools for RNA-seq analysis and interpretation
Script for basic DESeq2 analysis: http://geeleherlab.org/teachingFiles/dEseq2Test.R
Script for creating usable breast cancer expression dataset from files downloaded from GDC: http://geeleherlab.org/teachingFiles/loadBrcaData.R
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
Gene set database file for GSEA: http://geeleherlab.org/teachingFiles/c5.bp.v7.1.symbols.gmt