omicverse.single.pySCSA

omicverse.single.pySCSA(adata: AnnData, foldchange: float = 1.5, pvalue: float = 0.05, output: str = 'temp/rna_anno.txt', model_path: str = '', outfmt: str = 'txt', Gensymbol: bool = True, species: str = 'Human', weight: int = 100, tissue: str = 'All', target: str = 'cellmarker', celltype: str = 'normal', norefdb: bool = False, cellrange: str = None, noprint: bool = True, list_tissue: bool = False, tissuename: str = None, speciename: str = None) → None[source]

Automated cell-type annotation using SCSA marker-enrichment scoring.

Parameters:

  • adata (anndata.AnnData) – Query AnnData for cell-type annotation.

  • foldchange (float, optional, default=1.5) – Fold-change cutoff for marker filtering.

  • pvalue (float, optional, default=0.05) – P-value cutoff for marker filtering.

  • output (str, optional, default='temp/rna_anno.txt') – Output path for SCSA annotation report.

  • model_path (str, optional, default='') – Path to local SCSA database/model.

  • outfmt (str, optional, default='txt') – Output format for intermediate annotation report.

  • Gensymbol (bool, optional, default=True) – Whether gene symbols are used as identifiers.

  • species (str, optional, default='Human') – Species used for marker database matching.

  • weight (int, optional, default=100) – Marker-weight scaling factor used by SCSA scoring.

  • tissue (str, optional, default='All') – Tissue filter for marker database query.

  • target (str, optional, default='cellmarker') – Marker database target (for example 'cellmarker' or 'panglaodb').

  • celltype (str, optional, default='normal') – Annotation context/type mode used by SCSA.

  • norefdb (bool, optional, default=False) – If True, skip reference database matching.

  • cellrange (str, optional, default=None) – Optional range/filter for cell selection.

  • noprint (bool, optional, default=True) – If True, suppress verbose console output.

  • list_tissue (bool, optional, default=False) – If True, list available tissues and exit.

  • tissuename (str, optional, default=None) – Compatibility alias for tissue.

  • speciename (str, optional, default=None) – Compatibility alias for species.

Returns:

Initializes SCSA annotation settings and database options.

Return type:

None

Examples

>>> # CRITICAL: Use clustertype='leiden', NOT cluster='leiden'!