mantispy.ds.jump_target2

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mantispy.ds.jump_target2#

mantispy.ds.jump_target2(plates=('1053600674', 'JCPQC051', 'BR00121438', 'ACPJUM012', '110000294936', 'CP1-SC1-25', 'A1170384', 'GR00003394', 'Dest210726-160150', 'LM37-70_1', 'CP-CC9-R1-29'), annotate=True, cache_dir=None)[source]#

JUMP-Target-2, one plate map run at many sites.

The JUMP consortium [Chandrasekaran et al., 2023] ran the same plate map in every participating laboratory, so differences between plates from different sources are technical. This makes it suited to studying batch and source effects. All 141 of its plates in cpg0016-jump are pinned here, from eleven sources and 107 batches, which lets transport() separate a laboratory effect from a batch and a plate effect. source_9 ran it on 1536-well plates, the others on 384-well plates.

The default object (one plate from each of the eleven sources, annotated) is pre-built by scripts/build_staged_datasets.py and rehosted on scverse-exampledata, so the default call fetches a single h5ad. Any other plate selection, or annotate=False, still reads the raw per-plate profiles and backend count tables directly, so the batch-effect study can load any subset or all 141 plates.

Parameters:

  • plates (Sequence[str] | None (default: ('1053600674', 'JCPQC051', 'BR00121438', 'ACPJUM012', '110000294936', 'CP1-SC1-25', 'A1170384', 'GR00003394', 'Dest210726-160150', 'LM37-70_1', 'CP-CC9-R1-29'))) – Plate barcodes to load. The default takes one plate from each source; None loads all 141, 9.4 GB.

  • annotate (bool (default: True)) – Join the JUMP annotation, which supplies Metadata_Perturbation and Metadata_Control. Downloads another 14 MB.

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

Return type:

AnnData

Returns:

One row per well at well resolution, carrying Metadata_Source, Metadata_Batch, Metadata_Plate, Metadata_Well, Metadata_CellCount, Metadata_SiteCount and, when annotated, Metadata_JCP2022, Metadata_Perturbation, Metadata_Perturbation_Type ("compound"), Metadata_InChIKey and Metadata_Control (the DMSO wells). The default call is read with mantispy.io.read(); any other selection is assembled from the raw tables.

Raises:

KeyError – A plate is not one of the 141.

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