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).
Data fileThe 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 codeThe following file is output from knitr("edgeRQL.Rnw", tangle=TRUE) and gives just the R commands used in the workflow:
LaTeX and knitr filesThe following files can be used to automatically perform the data analysis (using Bioconductor 3.3) and to generate the article LaTeX file:
- edgeRQL.Rnw: run knit() on this file to produce the LaTeX file.
- f1000_styles2.sty: LaTeX style file.
- QualityScores.png: LaTeX figure file.
- ref.bib: LaTeX BibTeX file.
Preprint of articleThe above files produce the following pdf article (after running knitr, BibTeX and pdfLaTeX):
Comments/Questions? Contact Gordon Smyth.
Last modified: 21 July 2016