mantispy.ds.oasis_pilot

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mantispy.ds.oasis_pilot#

mantispy.ds.oasis_pilot(annotate=True, cache_dir=None, **kwargs)#

OASIS pilot, 4,604 wells in U2OS and HepaRG, most compounds over a ten-point dose range.

cpg0033-oasis-pilot, twelve plates read down to the features they share, over four batches: two of assay development and two that dose 36 compounds in each cell line. It is the dose-response dataset of the package: 28 of those compounds carry six or more concentrations in both U2OS and HepaRG.

Parameters:

  • annotate (bool (default: True)) – Join the plate maps, which supply Metadata_Compound, Metadata_Concentration, Metadata_CellLine, Metadata_Control (the DMSO wells) and Metadata_Perturbation.

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

  • kwargs (Any) – Passed to mantispy.io.read_profiles().

Return type:

AnnData

Returns:

Wells by features, indexed by plate and well, with Metadata_CellCount and Metadata_SiteCount, and the annotation columns above when annotate.

Notes

The four batches name their plate-map columns differently, so the join reads whichever of treatment/Compound Name/compound and concentration_uM/assay_conc_uM/compound_concentration each one carries. Concentrations are micromolar.

The assay-development batch doses DMSO itself, so a control well there carries a concentration. Metadata_Control marks the compound, not the dose.

Two of the plate maps write the dose to three decimals and the rest to four, so one concentration is recorded as both 3.704 and 3.7037. Metadata_Concentration keeps what was recorded; Metadata_ConcentrationNominal puts the levels that agree to within 1% onto the value the most wells carry, and names the replicate groups. Group by the raw column and a treatment’s wells split in two.

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