mantispy.ds.aconcagua

mantispy.ds.aconcagua(cache_dir=None)

Aconcagua, the Brieflow reanalysis of an optical pooled CRISPR screen of 5,072 fitness-conferring genes in HeLa cells.

One row per guide per well: the median profile of a guide’s cells in a well, after a per plate-and-well robust normalization against the well’s non-targeting controls, over a subset of the screen built for the optical-pooled-screens case study. The cells were segmented and measured with brieflow’s cp_emulator in four channels (DNA, alpha-tubulin, gamma-H2AX and F-actin); the brieflow feature names are mapped to mantispy’s CellProfiler-style grammar. The subset keeps all 250 non-targeting guides, four annotated positive controls (H2AX, ECT2, TUBB, CFL1), 50 strong and 50 weak known hits, and 396 random library genes, across eight plates and 46 wells.

Mitotic cells are pooled at their natural share rather than capped, so a profile mixes interphase and mitotic cells as the screen saw them, and each row records its Metadata_MitoticFraction. The file is staged on scverse-exampledata, so the loader fetches a single h5ad; scripts/build_aconcagua.py rebuilds it from the public per-cell table.

Parameters:

cache_dir str | Path | None (default: None)

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

Return type:

AnnData

Returns:

Guide-by-well profiles read with mantispy.io.read(), carrying Metadata_Plate, Metadata_Well (and its Metadata_Row and Metadata_Col), Metadata_sgRNA, Metadata_Gene, Metadata_Perturbation (the gene, or "nontargeting"), Metadata_Perturbation_Type ("crispr"), Metadata_Control and Metadata_Control_Type (negcon/poscon/treatment), Metadata_Tier (control/positive_control/strong/weak/random), Metadata_CellCount, Metadata_SiteCount and Metadata_MitoticFraction.

References

Di Bernardo and others [2026], the Brieflow reanalysis; [Funk et al., 2022], the screen it reanalyses. The per-cell measurements are from brieflow; the subset is available through the CZ Biohub OPS Explorer.