Reproducible Research

Martin Morgan
February 3, 2015

Importance of reproducibility

A cautionary tale

Facilities enabling reproducible analysis in R

Basics – quickly becomes unsatisfactory

Vignettes – 'literate programming'

More advanced considerations

Version control



Produce a short 'vignette' summarizing your RNA-seq work yesterday. The code chunks might be along the lines of



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.