sccross.data.geneActivity

sccross.data.geneActivity(adata, gtf_file='./reference/gencode.vM30.annotation.gtf', upstream=2000, feature_type='transcript', annotation='HAVANA', raw=False)[source]

Gene activity score calculation

Parameters

  • adata (AnnData) – Input dataset

  • gtf_file – GTF reference path

  • upstream – upstream finding

  • feature_type – feature type

  • annotation – annotation type

  • raw – raw data or not

Return type

AnnData

Returns

AnnData – Gene activity score data with shape \(n_{cell} \times n_{gene}\)