omicverse.single.Drug_Response

omicverse.single.Drug_Response(adata, scriptpath, modelpath, output='./', model='GDSC', clusters='All', cell='A549', cpus=4, n_drugs=10)[source]

Predict drug sensitivity from single-cell transcriptomes using CaDRReS models.

Parameters:

  • adata (AnnData) – Query single-cell AnnData.

  • scriptpath (str) – Path to CaDRReS-Sc scripts.

  • modelpath (str) – Path to pretrained pharmacogenomic model/data resources.

  • output (str, optional) – Output directory for prediction tables and plots.

  • model ({'GDSC', 'PRISM'}, optional) – Pharmacogenomic reference model.

  • clusters (str, optional) – Cluster subset to analyze ('All' uses all cells).

  • cell (str, optional) – Cell-line context used by the model.

  • cpus (int, optional) – CPU threads used by downstream steps.

  • n_drugs (int, optional) – Number of top drugs to report/plot.

Returns:

Initializes drug-response prediction workflow state.

Return type:

None

Examples

>>> job = ov.single.Drug_Response(adata, scriptpath="CaDRReS-Sc")