AnnData | MuData, features: DataFrame | None = None, stranded: bool = False, extend_upstream: int = 2000.0, extend_downstream: int = 0) AnnData#

Count fragments overlapping given Features. Returns cells x features matrix.


AnnData object with peak counts or multimodal MuData object with ‘atac’ modality.


A DataFrame with feature annotation, e.g. genes. Annotation should contain columns (case-insensitive): chr/chrom/chromosome (longer takes precedence), start, end.


Use strand information for each feature. Has to be encoded as a “strand” (case-insensitive) column in features. When stranded=True, extend_upsteam and extend_downstream will be used according to each feature’s strand information.


Number of nucleotides to extend every gene upstream (2000 by default to extend gene coordinates to promoter regions)


Number of nucleotides to extend every gene downstream (0 by default)