On 5/22/24 02:16, Vincent Carey wrote:
> ...
>
> > Q4: Do you think a separate ExperimentData package satisfying
> the specifications laid out in Background 2 is warranted? This
> could be included in a future version with
> SummarizedExperiment/MetaboExperiment support.
>
Dear Vilhelm,
If you need to use/share (reasonably large) MS data, you could consider
contributing data to the MsDataHub package [1], that is superseding msdata and
makes use of ExperimentHub. Feel free to get in touch (ideally opening a
GitHub) if this is of interest to you.
Best wishes,
Really glad to see this discussion moving forward. I would say that the
core is wrangling with some
even lower-level technical concerns right now, so I can't jump in just
now. I just want to raise the question
of whether bigWig files are a technologically sound format to continue
investing in
Thanks for sharing Leo, this does interest me, especially since so much is
built on BigWig access via rtracklayer at least in the recount2 ecosystem.
As you alluded to, Megadepth currently supports remote access of BigWigs
(and BAMs) over HTTPS on all platforms (Linux, MacOS, and Windows),
>
> ...
>
> > Q4: Do you think a separate ExperimentData package satisfying the
> specifications laid out in Background 2 is warranted? This could be
> included in a future version with SummarizedExperiment/MetaboExperiment
> support.
> It depends on the size of the data. For a software package,
Dear Vilhelm,
notame seems to be an interesting package filling some gaps that currently
exist in the untargeted metabolomics workflow. I would strongly suggest to
support the SummarizedExperiment classes (in future). I would maybe suggest to
keep it as generic as possible without dedicated
