sfaira.data.Universe

class sfaira.data.Universe(data_path: Optional[str] = None, meta_path: Optional[str] = None, cache_path: Optional[str] = None, exclude_databases: bool = True)

Attributes

adata
adata_ls
additional_annotation_key	"
datasets	Returns DatasetGroup (rather than self = DatasetSuperGroup) containing all listed data sets.
ids

Methods

collapse_counts()	Collapse count matrix along duplicated index.
download(**kwargs)
extend_dataset_groups(dataset_groups)
flatten()	Returns DatasetGroup (rather than self = DatasetSuperGroup) containing all listed data sets.
get_gc([genome])
load([annotated_only, load_raw, ...])	Loads data set homosapiens into anndata object.
load_config(fn)	Load a config file and recreates a data sub-setting.
ncells([annotated_only])
ncells_bydataset([annotated_only])	List of list of length of all data sets by data set group.
ncells_bydataset_flat([annotated_only])	Flattened list of length of all data sets.
project_celltypes_to_ontology([...])	Project free text cell type names to ontology based on mapping table.
remove_duplicates([supplier_hierarchy])	Remove duplicate data loaders from super group, e.g.
set_dataset_groups(dataset_groups)
show_summary()
streamline_features([match_to_release, ...])	Subset and sort genes to genes defined in an assembly or genes of a particular type, such as protein coding.
streamline_metadata([schema, clean_obs, ...])	Streamline the adata instance in each group and each data set to output format.
subset(key, values)	Subset list of adata objects based on match to values in key property.
subset_cells(key, values)	Subset list of adata objects based on cell-wise properties.
write_config(fn)	Writes a config file that describes the current data sub-setting.
write_distributed_store(dir_cache[, ...])	Write data set into a format that allows distributed access to data set on disk.