mantispy.ds.aconcagua_cells

mantispy.ds.aconcagua_cells(cache_dir=None)

Single cells of eight genes of the aconcagua() screen and its non-targeting controls, in HeLa cells.

The genes are RRM1, DTL, SKA2, HAUS6, ITGAV, TLN1, PSMB7 and SF3B3. The cells were imaged in four channels: DAPI for DNA, gamma-H2AX, phalloidin for actin, and alpha-tubulin. Intensities are raw, as brieflow measured them, so mantispy.tl.dna_content() can read the DNA stain. Every extracted cell of the eight genes is kept, with its mitotic cells uncapped; the non-targeting controls are a tenth, sampled at random, for 38,674 cells in all.

Parameters:

cache_dir str | Path | None (default: None)

Where to keep the download. Defaults to mantispy.settings.cache_dir.

Return type:

AnnData

Returns:

Cells by features at object resolution, read with mantispy.io.read(), carrying Metadata_Plate, Metadata_Well (and its Metadata_Row and Metadata_Col), Metadata_Site, Metadata_ObjectNumber, Metadata_sgRNA, Metadata_Gene, Metadata_Perturbation (the gene, or "nontargeting"), Metadata_Perturbation_Type ("crispr"), Metadata_Control, Metadata_Control_Type and the screen’s interphase or mitotic call per cell, Metadata_Class.

References

Di Bernardo and others [2026], the Brieflow reanalysis; [Funk et al., 2022], the screen it reanalyses.