[Bioc-devel] Workflows for Bioconductor channel at F1000R

Wolfgang Huber whuber at embl.de
Thu Jun 2 09:42:19 CEST 2016


I’m giving my reply via the Bioconductor mailing list to also include the others, both for input from the core team, and for information of other workflow authors.

The preferred approach is to host a live version of the workflow on http://www.bioconductor.org/help/workflows/ - with the obvious advantages of easy installation for users (e.g. http://www.bioconductor.org/help/workflows/rnaseqGene) and continuous testing.

The .Rmds are (and can be maintained by the authors) at https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows . The Bioconductor project is moving from subversion to github, maybe Martin or someone can outline the ramifications, if any, for authors.

To get the document from there into F1000R, Mike Love made notes: https://docs.google.com/document/d/1SC1Z6TS6eepNelu4Eyng7cdbJBMXzZZoMOzfLEYe0LE/edit
The main effort being in manually uploading the figures to Overleaf​ and in manually adding figure captions. I wish this could be further automated.

Kind regards

Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)

> On 1 Jun 2016, at 16:52, Susan Holmes <susanatstat at gmail.com> wrote:
> Hi there,
> So I a managed to get our workflow paper in before midnight last night (it is quite long, mainly because of the pictures), I am in touch with their office through
> someone called Paola and she says they prefer a GitHub repository,
> did you do that? Is there a preferred directory/document structure?
> Should I make a Bioconductor Workflow like document to publish alongside?
> Best
> Susan
> Susan Holmes
> Professor, Statistics and BioX
> John Henry Samter University Fellow
> coDirector, Math Comp Sci
> 102, Sequoia Hall,  
> 390 Serra Mall,
> Stanford
> http://www-stat.stanford.edu/~susan/
> <f1000research-revisions-bioconductor.pdf>

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