pycea.datasets.koblan25

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pycea.datasets.koblan25#

pycea.datasets.koblan25(experiment='tumor', cache_dir='~/.treedata/datasets')#

Spatially resolved lineage tracing of 4T1 tumors [KYZ+25].

This study presents PEtracer, a novel prime editing-based lineage tracer that can be read out using either scRNA-seq or spatial imaging. PEtracer is validated in vitro using sequential rounds of static barcoding and applied in vivo to study the 4T1 transplantable mouse breast cancer model. The tumor dataset contains malignant cells with lineage information as well as stromal and immune cells.

Parameters:

  • experiment (str (default: 'tumor')) –

    • “tumor”: Loads in vivo data from mouse 3 tumor 1.

    • ”barcoding”: Loads in vitro barcoding data from clone 4.

  • cache_dir (PathLike | str (default: '~/.treedata/datasets')) – The directory where the datasets are cached. Default is ~/.treedata/datasets.

Return type:

TreeData

Returns:

TreeData object.

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