omicverse.single.Annotation#
- class omicverse.single.Annotation(adata)[source]#
Unified single-cell annotation manager for cell-type labeling.
- Parameters:
adata (AnnData) – Query single-cell AnnData to annotate.
- Returns:
Initializes annotation manager state and reference caches.
- Return type:
None
- __init__(adata)[source]#
Initialize annotation manager with a query AnnData object.
- Parameters:
adata (AnnData) – Query dataset to annotate.
Methods
__init__(adata)Initialize annotation manager with a query AnnData object.
add_reference_pkl(reference)Register a CellTypist model file for supervised annotation.
add_reference_sc(reference[, celltype_key])Register a single-cell reference atlas for transfer-based annotation.
add_reference_scsa_db(reference)Register a local SCSA marker database file.
annotate([method, cluster_key])Annotate cells or clusters using the selected annotation backend.
download_reference_pkl(reference_name, save_path)Download a CellTypist model by model name and store it locally.
download_scmulan_ckpt([save_path, ...])Download the pretrained scMulan checkpoint.
download_scsa_db([save_path])Download SCSA database with fallback mirrors.
query_reference([source, data_desc, ...])Use an LLM to identify relevant reference resources based on a description.