[Bioc-devel] Bioc workflows: using rmarkdown as vignette engine

Michael Love michaelisaiahlove at gmail.com
Fri Aug 14 19:29:18 CEST 2015

hi Dan,

(I add bioc-devel as this might be useful info for others)

Is it possible to specify rmarkdown as the vignette engine for workflows?

The citation functionality [1] of rmarkdown would be useful, as there
is discussion to have workflows possible submitted as peer reviewed

I tried adding:


as recommended here [2] but the auto package builder adds this on top:


and my test of using a citation fails [3] (although locally running
rmarkdown::render(), the citation and bibliography works). My test
citation look like: [@love2014]



[1] http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html
[2] http://www.bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
[3] http://bioconductor.org/help/workflows/rnaseqGene/

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