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., 2024].

Parameters:

• adata (AnnData) – AnnData object containing data.

• use_rep (Optional[str]) – Layer name containing labeled mRNA data.

• time_key (str) – Column in adata.obs with labeling time of observations.

• experiment_key (str) – Column in adata.obs with experimt type of observations.

• n_neighbors – TODO

• x0 (List[float]) – 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).