Add anndata container as an output format

nf-core / molkart

A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

https://nf-co.re/molkart

MIT License

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Add anndata container as an output format #26

Closed FloWuenne closed 9 months ago

FloWuenne commented 11 months ago

Description of feature

Instead of just providing the quantified cell table, we could support export of data in the popular Anndata format as described in the Squidpy documentation:

https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/tutorial_read_spatial.html

This would facilitate easy downstream usage of Liana+ and other anndata compatible frameworks.

FloWuenne commented 9 months ago

Added with #49 !