mantispy.ds.jump_target2

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mantispy.ds.jump_target2#

mantispy.ds.jump_target2(plates=('BR00121438', 'JCPQC051'), annotate=True, cache_dir=None)[source]#

JUMP-Target-2, one 384-well plate map run at many sites.

The JUMP consortium 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. Twelve of the 141 plates in cpg0016-jump are pinned here (three sources, two batches each, two plates per batch), which lets transport() separate a laboratory effect from a plate effect.

Parameters:

  • plates (Sequence[str] | None (default: ('BR00121438', 'JCPQC051'))) – Plate barcodes to load. The default takes one plate from each of two sources, about 26 MB; None loads all twelve.

  • 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:

384 wells per plate at well resolution, carrying Metadata_Source, Metadata_Batch, Metadata_Plate, Metadata_Well and, when annotated, Metadata_JCP2022, Metadata_Perturbation, Metadata_InChIKey and Metadata_Control (JUMP’s 64 DMSO wells per plate).

Raises:

KeyError – A plate is not one of the twelve.

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