Remove dependencies on Giotto objects

Nanostring-Biostats / FastReseg

FastReseg for detection and correction of cell segmentation error based on spatial profile of transcripts.

https://nanostring-biostats.github.io/FastReseg/

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Remove dependencies on Giotto objects #5

Closed patrickjdanaher closed 2 years ago

patrickjdanaher commented 2 years ago

Background

The TAP and the commercial DA will both use Seurat objects rather than Giotto objects. But exactly the format of that Seurat object remains to be determined.

Takeaways:

FastReseg shouldn't ever rely on a Giotto object
It's not yet time to incorporate a Seurat object into FastReseg.
My sense if that FastReseg only uses the giotto object for things like cell type and maybe cell type profiles. We can input this info to FastReseg as vectors and matrices.

patrickjdanaher commented 2 years ago

Actually, it's fine, since we don't depend on a giotto object; we just use giotto functions.