Slingshot followed by CellRank

[Yanst86]

Hi,

I performed a Slingshot analysis on my Seurat data in R, and would like to import the output to CellRank in Python for a follow up analysis. However, I failed to convert the singlecellexperiment object I have to Anndata using various tools, including zellkonverter, sceasy and scDIOR. I figured there could be another approach - to convert my Seurat object to anndata and run Slingshot in Python. Anyone here have an experience with this transition and could recommend what worked for him/her?

Thanks, Yan

[kstreet13]

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