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scverse / scanpy

Single-cell analysis in Python. Scales to >1M cells.
https://scanpy.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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d = sce.tl.palantir(adata) returns "None" #1237

Closed zmokhtari closed 11 months ago

zmokhtari commented 4 years ago

Hi, Thanks for providing an amazing platform for single-cell data analysis. I was trying to use palantir in scanpy and I just reran the example data. However, d = sce.tl.palantir(adata) always return None for any kind of data. Could you please comment on this? I am using scanpy 1.5 and have updated Palantir to 0.2.6 Thanks in advance, Zeinab

kousaa commented 4 years ago

I am facing the same issue. I have recently updated my scanpy to the latest version. I think that it was working before that.

Here is rest of my software versions scanpy==1.4.6 anndata==0.7.1 umap==0.3.9 numpy==1.17.4 scipy==1.3.1 pandas==0.25.3 scikit-learn==0.22 statsmodels==0.10.1 python-igraph==0.7.1 louvain==0.6.1

gokceneraslan commented 4 years ago

@awnimo can you have a look?

awnimo commented 4 years ago

@gokceneraslan

A fix is provided here https://github.com/theislab/scanpy/pull/1245

In the meanwhile until this PR is merged into a new release you can follow this https://github.com/dpeerlab/Palantir/issues/34#issuecomment-632933449

eroell commented 11 months ago

Just came across this, look like it has been fixed - thanks everyone involved back then!