[Bioc-devel] biocViews - Spatial

[Kern, Lori]

SpatialData is a term that is showing up for me under ExperimentData/TechnologyData/SequencingData/:
https://bioconductor.org/packages/devel/BiocViews.html#___SpatialData

I expect to see spatialLIBD to appear under it within the next 24-48 hours.

Cheers,


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Leonardo Collado Torres <lcolladotor using gmail.com>
Sent: Wednesday, January 26, 2022 2:29 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: Lukas Weber <lukas.weber.edu using gmail.com>; bioc-devel using r-project.org <bioc-devel using r-project.org>; Stephanie Hicks <shicks19 using jhu.edu>
Subject: Re: [Bioc-devel] biocViews - Spatial

Hi Lori and bioc-devel,

Unless I'm missing something, I don't see SpatialData at https://bioconductor.org/packages/devel/BiocViews.html<https://secure-web.cisco.com/1V9nJvlPlt3AINsdZqrhTR0QlQItCZzi8RPzURvCoLauy-ybO5mgD6mBwk5ne8jRiVpoYOJqpiMCRgAEtMaAK55F5nm3Gt-pXmNA15aazaLdmCmoHl_d6tb7Rf9gDLitKuvEZ2TRKJfvkUjH7duYwMBPifn4HlHKdgB_Ud2znx1kfTQg_s7Ik6Ms6Y3i_Ec86PXcoloe2wF10Q0QvLRvtLF3sAx0dFoo3hkEGFImmazdiGsMSgKOM6WwJwXS7BEjuCQBA-1-DCCvUUfDqTsippOASNFyq0w1bepnkb5w0WQlf-n12oY-9k5y9WfPYNmBtylNYNWQd1wOnxKj36QzBxQ/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2FBiocViews.html> (with the option to show childless terms). I just added it anyways to spatialLIBD at https://github.com/LieberInstitute/spatialLIBD/commit/dbeba1dd80bebac7fd8ef6422b5e995f080046a3<https://secure-web.cisco.com/1yUzPwkm03NWYhX6zR3HyCqVY8TIBmZY23IMtVN9LKOZ-Cayg_fFLwl5S2Z2yJCDj-jVEzb2bC6Cw1uY1Z1i-TuROhy1Mbpqr3jY2DZ9tkXcE2pvlN6OLd2jr2dpFLILscQaKU7-VFuK9NQWZAoX2i0ZurjpWnwhiHsjttYay6ofpdtrbzdE1B2eKh-pFC-dZZTOY_SQc1PbvMBolP4Df0CueN-jdla-kHaBB-go2SwrTd0TInb23Y-E4mfCH3E8Y5yselKQjPvMnNvlnnfiy1EjzLmiuRKWSpBLx0aVmQUvztQ2g5VsldOl2mB67_neEnF4rlvEFHFGbN6epFJRHUw/https%3A%2F%2Fgithub.com%2FLieberInstitute%2FspatialLIBD%2Fcommit%2Fdbeba1dd80bebac7fd8ef6422b5e995f080046a3>.

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
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Baltimore, MD 21205
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On Fri, Jul 30, 2021 at 9:48 AM Kern, Lori <Lori.Shepherd using roswellpark.org<mailto: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<mailto:bioc-devel-bounces using r-project.org>> on behalf of Lukas Weber <lukas.weber.edu using gmail.com<mailto:lukas.weber.edu using gmail.com>>
Sent: Thursday, July 29, 2021 3:29 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Cc: Stephanie Hicks <shicks19 using jhu.edu<mailto: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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