February 3, 2015
A cautionary tale
Basics – quickly becomes unsatisfactory
Vignettes – 'literate programming'
Produce a short 'vignette' summarizing your RNA-seq work yesterday. The code chunks might be along the lines of
library(airway) library(DESeq2) data(airway) dds <- DESeqDataSet(airway, design = ~ cell + dex) dds$dex <- relevel(dds$dex, "untrt") dds <- DESeq(dds) res <- results(dds)
Embed this in textual description with relevant descriptive information (title, author, date) as well as text describing nuances of each step, plus figures or tables of your choosing to illustrate relevant aspects of the experimental design or results.
Render this as an HTML document to share with your colleagues at home.