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

Wed, Dec 13, 2017 3:01 AM

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.

-A

On 12/12/17 22:11, Andrzej Ole? 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

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

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