mantispy.ds.pooled_rare

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mantispy.ds.pooled_rare#

mantispy.ds.pooled_rare(cache_dir=None, *, feature_selected=False)[source]#

Pooled rare variants, 290 barcodes in a pooled screen.

cpg0032-pooled-rare, aggregated to one row per barcode rather than per well, so there is no plate or well in obs.

The base and its feature-selected block are pre-built by scripts/build_staged_datasets.py from the raw gene-normalized table and rehosted on scverse-exampledata, so the loader fetches a single h5ad rather than reassembling it on every call.

Parameters:

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

  • feature_selected (bool (default: False)) – Return the block after pycytominer-default feature selection instead of all features.

Returns:

Metadata_Perturbation: the variant the barcode expresses (Metadata_Foci_Barcode_MatchedTo_GeneCode, 290 of them), the unit the library varied. It is a gene ("ACTB") or a specific coding variant of it ("ACTB E364K").

Metadata_Perturbation_Type: "orf", the variants being expressed from constructs.

Metadata_Gene (the gene the variant belongs to, the token before the first space) and Metadata_Allele (the full variant label).

Return type:

AnnData

Raises:

ValueError – feature_selected is not a bool.

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