theislab/scvelo

AttributeError: module 'scvelo' has no attribute 'pp'

Kalpi-ds opened this issue · 1 comments

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
# paste the error output here, if applicable
Versions
# paste the ouput of scv.logging.print_versions() here

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