[Bioc-devel] BiocStyle and R markdown

[Thomas Girke]

A simple formatting issue:

Since support for table of contents in R markdown vignettes has become
available, it seems like an amazing solution for many online
documentation needs in the future. 

What would help me to fully to adopt to it, is a solution to get rid of
the bullets in a numbered table of content which looks a bit unusual to
me: 
http://www.bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
For navigating longer documents numbered tables of contents are an
essential feature to me, which I believe wasn't available in earlier R
markdown versions or sometimes they showed up in unacceptable places
like before the title of a document.

A prescribed solution to get rid of these bullets from here 
http://stackoverflow.com/questions/28138456/rmarkdown-with-knitr-to-html-how-to-hide-bullets-in-toc-table-of-contents
didn't work for me. 

Also, it would be nice to be able to generate the exact same vignette
style in Bioc release and development, but it seems others have
difficulties with this too, probably due to version differences of R
markdown as seen here:
http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html

Thanks for making BiocStyle and R markdown available. I really enjoy
using them. The resulting HTML pages look professionally designed and
are highly functional while allowing us to focus on generating content
in a consistent format rather than getting lost in formatting issues. 

Thomas