[Bioc-devel] biocViews - Spatial

[Leonardo Collado Torres]

Hi Lori and bioc-devel,

Unless I'm missing something, I don't see SpatialData at
https://bioconductor.org/packages/devel/BiocViews.html (with the option to
show childless terms). I just added it anyways to spatialLIBD at
https://github.com/LieberInstitute/spatialLIBD/commit/dbeba1dd80bebac7fd8ef6422b5e995f080046a3
.

Though well, this is also making me think that it might be best for
spatialLIBD to change from an Experiment type package to a Software one for
visibility purposes. The code works equally well and well, it's tested
frequently enough.

Best,
Leo

Leonardo Collado Torres, Ph. D.
Investigator

LIEBER INSTITUTE *for* BRAIN DEVELOPMENT
855 N. Wolfe St., Suite 300
Baltimore, MD 21205
lcolladotor.github.io
lcolladotor using gmail.com



On Fri, Jul 30, 2021 at 9:48 AM Kern, Lori <Lori.Shepherd using roswellpark.org>
wrote:

> I think this is an acceptable proposal.  I will look at adding the
> biocViews to the devel version of Bioconductor for use.  They should be
> available for use by early next week once the new version of the biocViews
> packages builds and propagates on the build system.
>
> Cheers,
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Lukas
> Weber <lukas.weber.edu using gmail.com>
> Sent: Thursday, July 29, 2021 3:29 PM
> To: bioc-devel using r-project.org <bioc-devel using r-project.org>
> Cc: Stephanie Hicks <shicks19 using jhu.edu>
> Subject: [Bioc-devel] biocViews - Spatial
>
> Hi,
>
> I have a question about biocViews. Currently we are including packages for
> spatially resolved transcriptomics analysis in the SingleCell (and
> SingleCellData / SingleCellWorkflow) biocViews.
>
> Would it be possible to add a new biocViews for spatial data? We are likely
> to see a lot of new packages in this area in the coming years, so it could
> be useful to split them out from SingleCell.
>
> And if so, should we call it Spatial or SpatialTranscriptomics? (e.g. maybe
> having a more general Spatial would be better since this could also include
> spatial proteomics)
>
> So then I would imagine the following new biocViews, mirroring the current
> ones for SingleCell:
> - Spatial
> - SpatialData
> - SpatialWorkflow
>
> Do others have any views on this?
>
> Best regards,
> Lukas
>
> --
> Lukas M. Weber, Ph.D.
> Postdoctoral Fellow
> Department of Biostatistics
> Johns Hopkins Bloomberg School of Public Health
>
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