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Im trying to create a similar r package vignette as i have seen in DESeq2 (http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf). I like the table of contents and the links between it and the rest of the vignette, the page count, etc. It looks tidy and professional.

I have seen bits about knitrBootstrap (https://github.com/jimhester/knitrBootstrap) and buildVignettes (I can't post the link - third in one question - as a new member of Stackoverflow here - sorry!) but I don't think they are what I am looking for.

Is it possible to find an example format for DESeq2 vignette that I can easily tailor for my own package? Any advice is appreciated!

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    The source to the DESeq2 vignette is here: http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.Rnw – G. Grothendieck Oct 16 '14 at 03:31
  • The vignette is also at `with(vignette("DESeq2"), file.path(Dir, File))` – Martin Morgan Oct 16 '14 at 03:54
  • thanks to you both! do you think i would need to cite DESeq2 if i were to tailor their vignette, or is that pretty standardized vignette format? i am just wondering as both of you found the DESeq2 vignette itself, and not some original and shared and public vignette that DESeq2 authors had used. thanks for your ideas! –  Oct 16 '14 at 04:46
  • @G.Grothendieck, thanks for the link. I copied it into a .Rmd file in my Rstudio. However, when I tried to knit it into html, it looked very different (even some of the syntax was obviously not converting into the intended purposes). I am unsure how to troubleshoot that. –  Oct 16 '14 at 13:14
  • Have a look at the package source, i.e. the tar.gz file at http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html – G. Grothendieck Oct 16 '14 at 13:19
  • @G.Grothendieck, thanks. when i try the commands listed source("http://bioconductor.org/biocLite.R") and biocLite("DESeq2"), the second line causes a silence in RStudio (nothing happens, and I am stuck at the new line). I download the tar.gz file, but am unsure how to convert that to PDF. What I am trying to do is recreate the PDF file in RStudio. How can I accomplish this? I saved the code (http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.Rnw) into RStudio, but when I try to knit or pdf it, it does not look right. I tried File-->New-->R MarkDown –  Oct 16 '14 at 14:15

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