mantispy.ds.oasis_pilot

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mantispy.ds.oasis_pilot#

mantispy.ds.oasis_pilot(annotate=True, cache_dir=None, *, aggregated=False)[source]#

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.

The annotated base and its perturbation-level consensus are pre-built by scripts/build_staged_datasets.py from the raw profile and plate-map tables and rehosted on scverse-exampledata, so the loader fetches a single h5ad rather than joining the plate maps on every call. Passing annotate=False still reads the raw profiles directly, without the annotation join.

Parameters:

  • annotate (bool (default: True)) – Fetch the annotated base, which carries Metadata_Compound, Metadata_Concentration, Metadata_CellLine, Metadata_Control (the DMSO wells), Metadata_Perturbation and Metadata_Perturbation_Type ("compound"). False reads the raw profiles without the plate-map join and cannot be aggregated.

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

  • aggregated (bool (default: False)) – Return one modz consensus (Spearman, min_replicates=2) per Metadata_Perturbation instead of the wells, DMSO kept as the "DMSO" perturbation. Needs annotate=True.

Return type:

AnnData

Returns:

Wells by features at well resolution when aggregated is False, else the perturbation-level consensus, indexed by plate and well, with Metadata_CellCount and Metadata_SiteCount, read with mantispy.io.read(). The annotation columns above are present when annotate.

Raises:

ValueError – aggregated is not a bool, or aggregated is asked for with annotate=False.

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.

The plate maps disagree on precision: one batch writes the concentration the dilution produced, 0.0152416 uM, and another writes it rounded, 0.015. Metadata_Concentration is the dose the well was meant to get, reading a coarser spelling as the finer level it rounds to within each compound, and it names the replicate groups. Metadata_ConcentrationRecorded keeps what the plate map wrote: read against that column, every dosed compound here carries eighteen levels where ten were plated, and a treatment’s wells split across two spellings.

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