Datasets (sdq.datasets)#

sdq.datasets.larry
scdiffeq.datasets._larry_in_vitro.larry(data_dir: str = '/home/runner/work/scDiffEq/scDiffEq/docs/source', variant: str | None = None, filter_genes: bool = True, reduce_dimensions: bool = True, cytotrace: bool = True, force_download: bool = False) → AnnData[source]

LARRY in vitro dataset

Parameters:

  • data_dir – str, default=os.getcwd() Path to the directory where the data will be saved.

  • variant – Optional[str], default=None Dataset variant to download. None (default) downloads the full biology-rich dataset. “fate_prediction” downloads the original fate prediction dataset.

  • filter_genes – bool, default=True Whether to filter genes.

  • reduce_dimensions – bool, default=True Whether to reduce dimensions.

  • cytotrace – bool, default=True Whether to annotate LARRY with pre-computed CytoTRACE annotations.

  • force_download – bool, default=False Whether to force download the data.

Returns:

Preprocessed AnnData object.

Return type:

AnnData

More: sdq.datasets.larry

sdq.datasets.human_hematopoiesis
scdiffeq.datasets._human_hematopoiesis.human_hematopoiesis(data_dir: str = '/home/runner/work/scDiffEq/scDiffEq/docs/source', skip_scaling: bool = False, force_download: bool = False, download_unprocessed: bool = False) → AnnData[source]

Human hematopoiesis dataset

Parameters:

  • data_dir – str, default=os.getcwd() Path to the directory where the data will be saved.

  • skip_scaling – bool, default=False Whether to skip scaling.

  • force_download – bool, default=False Whether to force download the data.

  • download_unprocessed – bool, default=False Whether to download the unprocessed data.

Returns:

Preprocessed AnnData object.

Return type:

AnnData

More: sdq.datasets.human_hematopoiesis

sdq.datasets.pancreatic_endocrinogenesis
scdiffeq.datasets._pancreatic_endocrinogenesis.pancreatic_endocrinogenesis(data_dir: str = '/home/runner/work/scDiffEq/scDiffEq/docs/source', filter_genes: bool = True, reduce_dimensions: bool = True, force_download: bool = False, download_unprocessed: bool = False) → AnnData[source]

Pancreas dataset

Parameters:

  • data_dir – str, default=os.getcwd() Path to the directory where the data will be saved.

  • filter_genes – bool, default=True Whether to filter genes.

  • reduce_dimensions – bool, default=True Whether to reduce dimensions.

  • force_download – bool, default=False Whether to force download the data.

  • download_unprocessed – bool, default=False Whether to download the unprocessed data.

Returns:

Preprocessed AnnData object.

Return type:

AnnData

More: sdq.datasets.pancreatic_endocrinogenesis