mantispy.ds.jump_crispr

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mantispy.ds.jump_crispr#

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

The assembled JUMP CRISPR arm, 51,185 wells of knockouts in U2OS cells.

cpg0016-jump-assembled, the v1.0a well-position-corrected and feature-selected parquet. jump-profiling-recipe has corrected it for well position and cell count, normalized it and selected its features, and has not yet sphered it. The cell counts are the ones the recipe regresses out of these profiles; their Cells_Count_Count feature was normalized with the rest and is no longer a count.

The annotated base and its gene-level consensus are pre-built by scripts/build_staged_datasets.py from the raw parquet and rehosted on scverse-exampledata, so the loader fetches a single h5ad rather than reassembling the base 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 names the gene each well’s guides target and which wells are controls. False reads the raw profiles without the annotation 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_Gene over the guides instead of the wells. Needs annotate=True.

Return type:

AnnData

Returns:

Wells by features at well resolution when aggregated is False, else the gene-level consensus, indexed by plate and well, read with mantispy.io.read(), with Metadata_JCP2022 and Metadata_CellCount and, when annotated, Metadata_Gene and Metadata_Perturbation (the gene symbol; its guides are the replicates), Metadata_Perturbation_Type ("crispr"), Metadata_Control_Type ("negcon", "poscon" or "trt"), Metadata_Control (the no-guide and non-targeting wells) and Metadata_ChromosomeArm.

Raises:

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

References

Chandrasekaran et al. [2023].

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