Open grst opened 1 year ago
I would like to refactor a bit how AnnData objects are created and handled
adata.layers
. I'd be happy to put a PR together.
@fasterius / @cavenel WDYT?
Sounds good to me! I haven't really done any of the coding inside the reports, so don't have much to add - you'll have to ask @cavenel regarding your second point about the custom script. Might be due to legacy code from the Jackson Laboratory version of the pipeline, but that's just a guess.
With the latest updates to the pipeline I think that we fulfill your first two points @grst. Regarding the third point, do you mean "merge" as in some kind of integration or just something else?
I just mean storing all samples in a single SpatialData object rather than having one SpatialData object per sample.
Description of feature
Would be nice to have a single object instead of inidividual h5ad files. Optional batch correction for integration.