scvelo.inference.get_parameters

scvelo.inference.get_parameters(adata, use_rep, time_key, experiment_key, n_neighbors, x0, n_jobs=None)

Estimates parameters of splicing kinetics from metabolic labeling data.

See [Weiler et al., 2023].

adata

AnnData object containing data.

use_rep

Layer name containing labeled mRNA data.

time_key

Column in adata.obs with labeling time of observations.

experiment_key

Column in adata.obs with experimt type of observations.

n_neighbors

TODO

x0

The initial parameter estimate to use if provided.

n_job

Number of optimization problems to solve in parallel.

Returns

• Estimated parameters alpha (transcription rate), gamma (degradation rate), r0 (initial GEX if

• data from chase experiment is included), and success (flag if optimization ran successfully).