[Bioc-devel] biocViews - Spatial

Leonardo Collado Torres |co||@dotor @end|ng |rom gm@||@com
Wed Jan 26 20:29:20 CET 2022

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

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.


Leonardo Collado Torres, Ph. D.

855 N. Wolfe St., Suite 300
Baltimore, MD 21205
lcolladotor using gmail.com

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

> 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
>         [[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://secure-web.cisco.com/14dB-6vo-yjA4gE4ATcRw9dPs6-1AEapEW0fdBECs5-3WWDUXwQxUCHMMPLV6UDp0Fkom2ly3a1hPSLJFa143v7CvKrPC7jBmTxlDHxid_m9AK22RHiJ5AX7FiFRj8gt5ue_0t82yZC-Uk31UHjkk-34TgJ9RHx28tBRxzjqsGY_1hurxPJd6FCO_nG8Ge5WfY5VTLVKDWuigOaLwl9x9-OWkCizyMoC3vda3SzmmwY6BxTPS7XOiVA8REaRA3lNnXTnR8xYWYkbWnYx03ga8jxWJa7J6rhD3qAE6f_l3PEEQ-W0bFc191KfcnuRW2AkB/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>         [[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list