[Bioc-devel] splitting simpleSingleCell into self-contained vignettes

Aaron Lun alun at wehi.edu.au
Wed Dec 13 12:01:46 CET 2017

While we wait for the changes to come online: would you be open to PRs 
to workflow.md? I was thinking of making a nested list for the 
Introduction/part 1/part 2/part 3, which is a bit nicer to read.


On 12/12/17 22:11, Andrzej Oleś wrote:
> Thanks for you feedback Aaron!
> On Tue, Dec 12, 2017 at 9:49 PM, Aaron Lun <alun at wehi.edu.au 
> <mailto:alun at wehi.edu.au>> wrote:
>     Thanks Andrzej.
>     > Thank you. I've edited the workflow index page by introducing a separate
>     > "Single-cell Workflows" section, and by substituting the previous link to
>     > your workflow by links to the individual parts.
>     Great, I'm looking forward to seeing it. Do you know how frequently the
>     index page (I assume we're talking about
>     https://bioconductor.org/help/workflows/
>     <https://bioconductor.org/help/workflows/>) updates? I assume your edits
>     haven't propagated through the system yet.
> Not sure, should be online by now
> https://github.com/Bioconductor/bioconductor.org/commit/a60c46f0942d9825f9a643321890ba5987de109b
>     > As discussed during EuroBioc, I'm happy to restructure the index page by
>     > grouping workflows by topic. It would be really helpful if authors would
>     > chime in to suggest the most relevant sections for their workflows.
>     I can chip in with two that I'm involved in:
>     "Differential Binding from ChIP-seq data
>     <https://bioconductor.org/help/workflows/chipseqDB/
>     <https://bioconductor.org/help/workflows/chipseqDB/>>" => ChIP-seq
>     workflows
>     "Gene-level RNA-seq differential expression and pathway analysis
>     <https://bioconductor.org/help/workflows/RnaSeqGeneEdgeRQL/
>     <https://bioconductor.org/help/workflows/RnaSeqGeneEdgeRQL/>>" =>
>     RNA-seq
>     workflows
>     Of course, it depends on how granular you want the topics to be. For
>     example, I only see one ChIP-seq workflow, so that particular section
>     might be a bit lonely for a while (I am planning to split that into two
>     workflows later).
> Right, we should probably avoid hair-splitting. We can start with a few, 
> say 6, and split up further according to demand as new ones are introduced.
> Best,
> Andrzej

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