mantispy.ds.rohban

mantispy.ds.rohban(plates=None, cache_dir=None)

An ORF overexpression screen, with the genes and cell counts that BBBC021 lacks.

cpg0017-rohban-pathways: U2OS cells, one gene overexpressed per well, roughly ten replicate wells per gene over five plates. Downloads about 27 MB for all five.

Parameters:

• plates (Sequence[str] | None (default: None)) – Plate barcodes to load, all five when omitted.

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

Return type:

AnnData

Returns:

Wells by features at well resolution, with Metadata_Perturbation (the gene), Metadata_Control, Metadata_CellCount, Metadata_SiteCount and the screen’s own Metadata_gene_name, Metadata_GeneID and Metadata_ASSAY_WELL_ROLE.

Raises:

KeyError – A plate is not one of the five.

Notes

Metadata_Control marks the wells transfected with a control ORF (Luciferase, LacZ and eGFP), the reference for normalization. The untreated wells (Metadata_gene_name == "EMPTY") were never transfected and are not flagged; drop them if a gene-level analysis should not see them.

References

Rohban et al. [2017].