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Python APIHicSnHiCCellQC

SnHiCCellQC

class chr3d.SnHiCCellQC(
    min_contacts: int = 1000,
    min_complexity: float = 0.3,
    max_dup_rate: float = 0.8,
)

Quality control for individual sn-Hi-C cells.

Filters cells based on minimum contact counts and complexity metrics to remove low-quality cells before downstream analysis.

Parameters

ParameterTypeDescription
min_contactsintMinimum number of valid contacts required per cell (default: 1000)
min_complexityfloatMinimum library complexity (unique / total reads ratio) (default: 0.3)
max_dup_ratefloatMaximum duplicate rate allowed per cell (default: 0.8)

Methods

filter_cells

def filter_cells(
    self,
    cell_stats: Dict[str, Dict],
) -> Tuple[List[str], List[str]]

Filter cells based on QC metrics.

Parameters:

ParameterTypeDescription
cell_statsDict[str, Dict]Dict mapping cell_id → stats dict with keys: 'valid_contacts', 'duplicate_rate', 'complexity'

Returns:

Tuple[List[str], List[str]] — (passing_cell_ids, failing_cell_ids)

filter_cells is not yet fully implemented and will raise NotImplementedError.

Last updated on
SnHiCPipelineSnHiCPseudoBulk