scvelo for labeling data?

[wgao688]

Hi @WeilerP ,
I see the citation for metabolic labeling data for Weiler et al. and see the API (https://scvelo.readthedocs.io/en/stable/api.html) listing inference for metabolic labeling data, but I do not have access to those commands when I run scvelo 0.3.1 (python 3.10.13). Are the commands publicly available yet? Thanks!

[WeilerP]

Hi @wgao688, which part is not working? Everything works fine for me. A reproducible code snippet with a stack trace would be helpful.

[wgao688]

Hi Philipp, thanks for your response.

I am using scvelo v0.3.1 and have no issues following the tutorial (I know the dataset isn't a labeling experiment but wanted to start with that to confirm other functions are working on my end):

Installed via: pip install git+https://github.com/theislab/scvelo@main

import scvelo as scv
adata = scv.datasets.pancreas()
scv.pp.filter_and_normalize(adata)
scv.pp.moments(adata)
scv.tl.velocity(adata, mode='stochastic')
scv.tl.velocity_graph(adata)
scv.pl.velocity_embedding(adata, basis='umap')
scv.pl.velocity_embedding_grid(adata, basis='umap')
scv.pl.velocity_embedding_stream(adata, basis='umap')

This runs perfectly fine. However, if I try to run a command a like scv.inference.<command> (https://scvelo.readthedocs.io/en/stable/api.html#inference-from-metabolic-labeling-information), the option does not exist. I can run all other commands like scv.tl. or scv.pl., etc. So it's not that I get an error code, just that I don't see the functions available to run.

Am I using the wrong version of scvelo? Do you have a vignette available for labeling data? Thank you!

[WeilerP]

Sorry, what do you mean by "I don't see the functions available to run"? What is the exact traceback error when you try to import the functions? Can you import them?

The analysis done for the CellRank 2 preprint is shown here; the functions importable from scvelo.inference are set here.

[wgao688]

Hi Philipp, thanks for your help. From the links you provided, I see that I did not run this block after import scvelo as scv

from scvelo.inference import (
    get_labeling_time_mask,
    get_labeling_times,
    get_n_neighbors,
    get_obs_dist_argsort,
    get_parameters,
)

After that, I'm able to access to the functions (get_labeling_time_mask, etc.)