[Bioc-devel] [ext] Re: Vignettes for a data processing package

[Vincent Carey]

I think we can take this to a one-to-one discussion for now and report back
to bioc-devel.  I have
done a little work with the package and have some comments.

On Mon, Aug 5, 2019 at 1:16 PM Dermot Harnett <dermot.p.harnett using gmail.com>
wrote:

> Hi Vincent - thanks, much appreciated.
>
> Here's the current development version of the repository.
>
> https://github.com/ohlerlab/RiboseQC/
>
>
> <https://github.com/ohlerlab/RiboseQC/settings>
>
> On Mon, Aug 5, 2019 at 1:22 PM Vincent Carey <stvjc using channing.harvard.edu>
> wrote:
>
>> Is there an open github repository where this can be examined as a work
>> in progress?  If so please let us know and I and likely others will take a
>> look
>> and make recommendations.
>>
>> On Mon, Aug 5, 2019 at 6:55 AM Dermot Harnett <dermot.p.harnett using gmail.com
>> >
>> wrote:
>>
>> > Hi
>> > I've been put in charge of trying to clean up a package produced in my
>> lab
>> > into bioconductor compatible code.
>> >
>> > The package consists of a a few functions (which process annotation,
>> > process bam files, and then create a html report, respectively). Each of
>> > these functions necessarily take a long time aas they have to traverse a
>> > bam file several times, create lots of plots etc.
>> >
>> > It's proving extremely difficult, even with subsets of the data, to
>> create
>> > a vignette which can be run in the the bioconductor standard 10minutes.
>> > What would you recommend in these circumstances? Is it possible for the
>> > package to have a workflow vignette instead of a standard vignette?
>> >
>> > Best
>> > Dermot Harnett, PhD
>> > Ohler Group
>> > BIMSB, Berlin
>> >
>> >         [[alternative HTML version deleted]]
>> >
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>> >
>>
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