mantispy.ds.pki

mantispy.ds.pki(plates=None, cache_dir=None)

Kinase inhibitors over a dose series, from the JUMP pilot.

cpg0008-pki: fifteen compounds over a seven-point dose range (eleven at three doses, four at one) in U2OS cells, over eight plates with 32 to 64 replicate wells per treatment. Downloads about 71 MB for all eight.

Parameters:

• plates (Sequence[str] | None (default: None)) – Plate barcodes to load, all eight when omitted.

• cache_dir (str | Path | None (default: None)) – Where to keep the download. Defaults to mantispy.settings.cache_dir.

Return type:

AnnData

Returns:

Wells by features at well resolution, with Metadata_Perturbation (compound at concentration), Metadata_Compound, Metadata_Concentration (the platemap’s mmoles_per_liter), Metadata_MOA, Metadata_Control, Metadata_CellCount and Metadata_SiteCount.

Raises:

KeyError – A plate is not one of the eight.

Notes

Metadata_Control marks the DMSO wells only. The positive controls (Metadata_control_type == "poscon") are not flagged, because they are perturbations and should not be normalized against.