[Bioc-devel] biocViews - Spatial

Mon Jan 31 15:25:27 CET 2022

Awesome, thanks Lori! I see spatialLIBD as the sole entry of SpatialData
right now (hopefully there's more to come ^^).

Best,
Leo

On Thu, Jan 27, 2022 at 7:33 AM Kern, Lori <Lori.Shepherd using roswellpark.org>
wrote:

> 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
> 855 N. Wolfe St., Suite 300
> Baltimore, MD 21205
> lcolladotor.github.io
> <http://secure-web.cisco.com/1ygPQCh3ksxDNpBI5mGsOgpep4gup0q_MtXDL9GuXYFdV6LC3OZWjQBXHuhaC5s_SFQsRWo8PXVfIH9QfPy52ldmvi933Xmra1a8XcjkWtvQBC6eMZ3sAMaCx-UrkAqNaPG7YEaewg4I4bNQVY5tYpxVsppkwGdl1FJIZZA4-GfoUUxAUgPxB8Wv0E67g3mFb7h8D86s79p_BcqjOSGcm2XZbvj7ubZPBmJNgfM7gkkU--ap3ZsvXDbsdJe_P4q7FiXcQlwSSpcs9gY3UWMOB6kDmtpa78QynY6KMNlgP3PNFRMJgs8OLL3-NiKdRZ4pY/http%3A%2F%2Flcolladotor.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
>
> https://secure-web.cisco.com/10aorG4oGD4f2h4n5OS8ylJaxGAtMcxFS2Y2EFXjTrBSWAO3eyAIY1CE3LJ-weQNiZY9fyn47BjrGEtin5f0b4cQs-rzl2aETf6g_uYxTPWe_XcC8M6IF0izwGkVCx1allG9WDhfg3wzOIYi5VSLa4vGclgA2wwF3PMXdNh7G-Wb4tnecBRgJtrVvUsI_xl6g17F2aTvh9RHMwO0p4snxJsHL0FczcYtMiGxka305dfVi3j7D_b6bjXF4OK7qIqD3iU-9P-991pi8lfgVJ0_8UkoK2Jexb6VfT4VuLJYiy2umAKehzd40q6o7Yvf3NLBR/https%3A%2F%2Flmweber.org%2F
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