Supplementary Information for

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline

Yunshun Chen, Aaron T.L. Lun and Gordon K. Smyth

F1000Research 5, 1438 (2016).
http://f1000research.com/articles/5-1438

Data file

The only data file used by the workflow is the following tab-delimited text file describing the 12 samples. All other data that is analyzed is read automatically from the internet.

R code

The following file is output from knitr("edgeRQL.Rnw", tangle=TRUE) and gives just the R commands used in the workflow:

LaTeX and knitr files

The following files can be used to automatically perform the data analysis (using Bioconductor 3.3) and to generate the article LaTeX file:

Preprint of article

The above files produce the following pdf article (after running knitr, BibTeX and pdfLaTeX):

 


Comments/Questions? Contact Gordon Smyth.
Last modified: 21 July 2016