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):
Updates on Bioconductor websiteThe above files correspond to the article published in F1000Research in 2016. An updated version of the workflow, run with the latest version of edgeR and Bioconductor can be found on the Bioconductor website: "HTML" link to view the updated workflow. The updated workflow can be installed as a Bioconductor package.
Comments/Questions? Contact Gordon Smyth.
Last modified: 9 May 2018