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.

• targets.txt

R code

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

• edgeRQL.R

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:

• 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 article

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

• edgeRQL.pdf

Updates on Bioconductor website

The 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:

• Workflow Package: RnaSeqEdgeRQL

Follow the "HTML" link to view the updated workflow. The updated workflow can be installed as a Bioconductor package.

 

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Comments/Questions? Contact Gordon Smyth.
Last modified: 9 May 2018