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JEFworks-Lab / MERINGUE

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
https://jef.works/MERINGUE
GNU General Public License v3.0
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Create a Shiny package for handling spatial transcriptomics data #23

Open howtofindme opened 2 months ago

howtofindme commented 2 months ago

Hi, Wonderful job!

I have searched through many articles and am looking for a Shiny app that can handle spatial transcriptomics data in a similar manner to how Shinycell handles single-cell transcriptomics data.

However, currently, there is no R package available that fulfills this requirement.

However, I noticed that there is a function called makeApp in your R package that seems to be able to achieve this functionality. Since I am only familiar with using the Seurat package for spatial transcriptomics data analysis, would you be able to create an interface for the Seurat package so that Seurat objects can be used with makeApp to create Shiny apps? With the increasing depth of research in spatial transcriptomics, I believe this feature would greatly advance the field. Looking forward to your response. Best, Young

bmill3r commented 1 month ago

Hi @howtofindme,

Thanks for your suggestion! It is certainly a good idea but my bandwidth is pretty limited these days to try and implement this. But perhaps this is something to consider for future releases or other tools.

Thanks again, Brendan