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theislab / scvelo

RNA Velocity generalized through dynamical modeling
https://scvelo.org
BSD 3-Clause "New" or "Revised" License
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AttributeError: module 'scvelo' has no attribute 'pp' #1240

Closed Kalpi-ds closed 3 months ago

Kalpi-ds commented 3 months ago

Hi @WeilerP

When I am trying to run scv.pp.filter_and_normalize(NDN) I get the error "AttributeError: module 'scvelo' has no attribute 'pp'"

my annData objetc(NDN) looks like below. AnnData object with n_obs × n_vars = 14872 × 36601 obs: 'batch', 'cluster' var: 'Accession', 'Chromosome', 'End', 'Start', 'Strand' obsm: 'X_umap' layers: 'matrix', 'ambiguous', 'spliced', 'unspliced'

I generated this object by combining loom files and UMAP coordinates and cluster information from seurat object. I was following this tutorial https://github.com/basilkhuder/Seurat-to-RNA-Velocity

I have a feeling the NDN object might not be in the correct format. That's why I am getting the attribute error when try to run scvelo. I really appreciate if you can check the format and let me know what is missing here. Thank you in advance ...

# paste your code here, if applicable

scv.pp.filter_and_normalize(NDN)

Error output ```pytb # paste the error output here, if applicable ```
Versions ```pytb # paste the ouput of scv.logging.print_versions() here ```
WeilerP commented 3 months ago

That's an installation issue not an issue with the AnnData object. I suggest you install scvelo in a fresh conda environment.