iSEE for a SpatialExperiment

[cathalgking]

Can iSEE support Spatial transcriptomics data that is contained within a SPE (SpatialExperiment) object? I have 10x Visium data in an SPE and tried running iSEE(SPE) which opened a shiny app with no errors. However, there is no spatial image there so is there a way to format iSEE to include that?

[kevinrue]

Thanks for the question and the support!

Spatial functionality is on the roadmap but development (and maintenance of existing package) have become challenging without funding (and therefore time).

Unfortunately, we just heard back from a grant application that was not funded so we're back to the drawing board on this point.

We've heard of prototype panels developed by the community, so we're not a million miles away from making it happen.

[lcolladotor]

You might be interested in https://research.libd.org/spatialLIBD/reference/run_app.html in the meantime. See https://research.libd.org/spatialDLPFC/#interactive-websites for some actual examples (we have many other spatialLIBD apps out there too).