Comments (1)
kstreet13
commented on June 27, 2024
Hi @Yanst86,
I don't use python much, but there is a python implementation of Slingshot that you could try: https://pypi.org/project/pyslingshot/ (fair warning: I don't maintain this package and cannot verify it's accuracy). Depending on the specific outputs you need, you could also consider constructing your own SCE object that contains only the necessary results after running Slingshot.
Also, just to be clear, SingleCellExperiment objects are distinct from Seurat objects. There are probably methods for converting either of them to AnnData objects in python (and there are definitely methods for converting between the two), but it is impossible to run Slingshot on a Seurat object.
Best,
Kelly
from slingshot.
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