scranpyΒΆ
- scranpy package
- Submodules
- scranpy.adt_quality_control module
ComputeAdtQcMetricsResultsComputeAdtQcMetricsResults.__annotations__ComputeAdtQcMetricsResults.__dataclass_fields__ComputeAdtQcMetricsResults.__dataclass_params__ComputeAdtQcMetricsResults.__eq__()ComputeAdtQcMetricsResults.__hash__ComputeAdtQcMetricsResults.__match_args__ComputeAdtQcMetricsResults.__repr__()ComputeAdtQcMetricsResults.detectedComputeAdtQcMetricsResults.subset_sumComputeAdtQcMetricsResults.sumComputeAdtQcMetricsResults.to_biocframe()
SuggestAdtQcThresholdsResultsSuggestAdtQcThresholdsResults.__annotations__SuggestAdtQcThresholdsResults.__dataclass_fields__SuggestAdtQcThresholdsResults.__dataclass_params__SuggestAdtQcThresholdsResults.__eq__()SuggestAdtQcThresholdsResults.__hash__SuggestAdtQcThresholdsResults.__match_args__SuggestAdtQcThresholdsResults.__repr__()SuggestAdtQcThresholdsResults.blockSuggestAdtQcThresholdsResults.detectedSuggestAdtQcThresholdsResults.subset_sum
compute_adt_qc_metrics()filter_adt_qc_metrics()suggest_adt_qc_thresholds()
- scranpy.aggregate_across_cells module
AggregateAcrossCellsResultsAggregateAcrossCellsResults.__annotations__AggregateAcrossCellsResults.__dataclass_fields__AggregateAcrossCellsResults.__dataclass_params__AggregateAcrossCellsResults.__eq__()AggregateAcrossCellsResults.__hash__AggregateAcrossCellsResults.__match_args__AggregateAcrossCellsResults.__repr__()AggregateAcrossCellsResults.combinationsAggregateAcrossCellsResults.countsAggregateAcrossCellsResults.detectedAggregateAcrossCellsResults.indexAggregateAcrossCellsResults.sumAggregateAcrossCellsResults.to_summarizedexperiment()
aggregate_across_cells()
- scranpy.aggregate_across_genes module
- scranpy.analyze module
AnalyzeResultsAnalyzeResults.__annotations__AnalyzeResults.__dataclass_fields__AnalyzeResults.__dataclass_params__AnalyzeResults.__eq__()AnalyzeResults.__hash__AnalyzeResults.__match_args__AnalyzeResults.__repr__()AnalyzeResults.adt_filteredAnalyzeResults.adt_markersAnalyzeResults.adt_normalizedAnalyzeResults.adt_pcaAnalyzeResults.adt_qc_filterAnalyzeResults.adt_qc_metricsAnalyzeResults.adt_qc_thresholdsAnalyzeResults.adt_row_namesAnalyzeResults.adt_size_factorsAnalyzeResults.blockAnalyzeResults.clustersAnalyzeResults.column_namesAnalyzeResults.combined_pcaAnalyzeResults.combined_qc_filterAnalyzeResults.crispr_filteredAnalyzeResults.crispr_markersAnalyzeResults.crispr_normalizedAnalyzeResults.crispr_pcaAnalyzeResults.crispr_qc_filterAnalyzeResults.crispr_qc_metricsAnalyzeResults.crispr_qc_thresholdsAnalyzeResults.crispr_row_namesAnalyzeResults.crispr_size_factorsAnalyzeResults.graph_clustersAnalyzeResults.kmeans_clustersAnalyzeResults.mnn_correctedAnalyzeResults.rna_filteredAnalyzeResults.rna_gene_variancesAnalyzeResults.rna_highly_variable_genesAnalyzeResults.rna_markersAnalyzeResults.rna_normalizedAnalyzeResults.rna_pcaAnalyzeResults.rna_qc_filterAnalyzeResults.rna_qc_metricsAnalyzeResults.rna_qc_thresholdsAnalyzeResults.rna_row_namesAnalyzeResults.rna_size_factorsAnalyzeResults.snn_graphAnalyzeResults.to_singlecellexperiment()AnalyzeResults.tsneAnalyzeResults.umap
analyze()
- scranpy.build_snn_graph module
GraphComponentsGraphComponents.__annotations__GraphComponents.__dataclass_fields__GraphComponents.__dataclass_params__GraphComponents.__eq__()GraphComponents.__hash__GraphComponents.__match_args__GraphComponents.__repr__()GraphComponents.as_igraph()GraphComponents.edgesGraphComponents.verticesGraphComponents.weights
build_snn_graph()
- scranpy.center_size_factors module
- scranpy.choose_highly_variable_genes module
- scranpy.choose_pseudo_count module
- scranpy.cluster_graph module
ClusterGraphLeidenResultsClusterGraphLeidenResults.__annotations__ClusterGraphLeidenResults.__dataclass_fields__ClusterGraphLeidenResults.__dataclass_params__ClusterGraphLeidenResults.__eq__()ClusterGraphLeidenResults.__hash__ClusterGraphLeidenResults.__match_args__ClusterGraphLeidenResults.__repr__()ClusterGraphLeidenResults.quality
ClusterGraphMultilevelResultsClusterGraphMultilevelResults.__annotations__ClusterGraphMultilevelResults.__dataclass_fields__ClusterGraphMultilevelResults.__dataclass_params__ClusterGraphMultilevelResults.__eq__()ClusterGraphMultilevelResults.__hash__ClusterGraphMultilevelResults.__match_args__ClusterGraphMultilevelResults.__repr__()ClusterGraphMultilevelResults.levelsClusterGraphMultilevelResults.modularity
ClusterGraphResultsClusterGraphWalktrapResultsClusterGraphWalktrapResults.__annotations__ClusterGraphWalktrapResults.__dataclass_fields__ClusterGraphWalktrapResults.__dataclass_params__ClusterGraphWalktrapResults.__eq__()ClusterGraphWalktrapResults.__hash__ClusterGraphWalktrapResults.__match_args__ClusterGraphWalktrapResults.__repr__()ClusterGraphWalktrapResults.mergesClusterGraphWalktrapResults.modularity
cluster_graph()
- scranpy.cluster_kmeans module
ClusterKmeansResultsClusterKmeansResults.__annotations__ClusterKmeansResults.__dataclass_fields__ClusterKmeansResults.__dataclass_params__ClusterKmeansResults.__eq__()ClusterKmeansResults.__hash__ClusterKmeansResults.__match_args__ClusterKmeansResults.__repr__()ClusterKmeansResults.centersClusterKmeansResults.clustersClusterKmeansResults.iterationsClusterKmeansResults.status
cluster_kmeans()
- scranpy.combine_factors module
- scranpy.compute_clrm1_factors module
- scranpy.correct_mnn module
CorrectMnnResultsCorrectMnnResults.__annotations__CorrectMnnResults.__dataclass_fields__CorrectMnnResults.__dataclass_params__CorrectMnnResults.__eq__()CorrectMnnResults.__hash__CorrectMnnResults.__match_args__CorrectMnnResults.__repr__()CorrectMnnResults.correctedCorrectMnnResults.merge_orderCorrectMnnResults.num_pairs
correct_mnn()
- scranpy.crispr_quality_control module
ComputeCrisprQcMetricsResultsComputeCrisprQcMetricsResults.__annotations__ComputeCrisprQcMetricsResults.__dataclass_fields__ComputeCrisprQcMetricsResults.__dataclass_params__ComputeCrisprQcMetricsResults.__eq__()ComputeCrisprQcMetricsResults.__hash__ComputeCrisprQcMetricsResults.__match_args__ComputeCrisprQcMetricsResults.__repr__()ComputeCrisprQcMetricsResults.detectedComputeCrisprQcMetricsResults.max_indexComputeCrisprQcMetricsResults.max_valueComputeCrisprQcMetricsResults.sumComputeCrisprQcMetricsResults.to_biocframe()
SuggestCrisprQcThresholdsResultsSuggestCrisprQcThresholdsResults.__annotations__SuggestCrisprQcThresholdsResults.__dataclass_fields__SuggestCrisprQcThresholdsResults.__dataclass_params__SuggestCrisprQcThresholdsResults.__eq__()SuggestCrisprQcThresholdsResults.__hash__SuggestCrisprQcThresholdsResults.__match_args__SuggestCrisprQcThresholdsResults.__repr__()SuggestCrisprQcThresholdsResults.blockSuggestCrisprQcThresholdsResults.max_value
compute_crispr_qc_metrics()filter_crispr_qc_metrics()suggest_crispr_qc_thresholds()
- scranpy.fit_variance_trend module
- scranpy.lib_scranpy module
aggregate_across_cells()aggregate_across_genes()build_snn_graph()center_size_factors()choose_highly_variable_genes()choose_pseudo_count()cluster_kmeans()cluster_leiden()cluster_multilevel()cluster_walktrap()combine_factors()compute_adt_qc_metrics()compute_clrm1_factors()compute_crispr_qc_metrics()compute_rna_qc_metrics()correct_mnn()filter_adt_qc_metrics()filter_crispr_qc_metrics()filter_rna_qc_metrics()fit_variance_trend()model_gene_variances()normalize_counts()perplexity_to_neighbors()run_pca()run_tsne()run_umap()sanitize_size_factors()scale_by_neighbors()score_gene_set()score_markers_pairwise()score_markers_summary()subsample_by_neighbors()suggest_adt_qc_thresholds()suggest_crispr_qc_thresholds()suggest_rna_qc_thresholds()summarize_effects()test_enrichment()
- scranpy.model_gene_variances module
ModelGeneVariancesResultsModelGeneVariancesResults.__annotations__ModelGeneVariancesResults.__dataclass_fields__ModelGeneVariancesResults.__dataclass_params__ModelGeneVariancesResults.__eq__()ModelGeneVariancesResults.__hash__ModelGeneVariancesResults.__match_args__ModelGeneVariancesResults.__repr__()ModelGeneVariancesResults.fittedModelGeneVariancesResults.meanModelGeneVariancesResults.per_blockModelGeneVariancesResults.residualModelGeneVariancesResults.to_biocframe()ModelGeneVariancesResults.variance
model_gene_variances()
- scranpy.normalize_counts module
- scranpy.rna_quality_control module
ComputeRnaQcMetricsResultsComputeRnaQcMetricsResults.__annotations__ComputeRnaQcMetricsResults.__dataclass_fields__ComputeRnaQcMetricsResults.__dataclass_params__ComputeRnaQcMetricsResults.__eq__()ComputeRnaQcMetricsResults.__hash__ComputeRnaQcMetricsResults.__match_args__ComputeRnaQcMetricsResults.__repr__()ComputeRnaQcMetricsResults.detectedComputeRnaQcMetricsResults.subset_proportionComputeRnaQcMetricsResults.sumComputeRnaQcMetricsResults.to_biocframe()
SuggestRnaQcThresholdsResultsSuggestRnaQcThresholdsResults.__annotations__SuggestRnaQcThresholdsResults.__dataclass_fields__SuggestRnaQcThresholdsResults.__dataclass_params__SuggestRnaQcThresholdsResults.__eq__()SuggestRnaQcThresholdsResults.__hash__SuggestRnaQcThresholdsResults.__match_args__SuggestRnaQcThresholdsResults.__repr__()SuggestRnaQcThresholdsResults.blockSuggestRnaQcThresholdsResults.detectedSuggestRnaQcThresholdsResults.subset_proportionSuggestRnaQcThresholdsResults.sum
compute_rna_qc_metrics()filter_rna_qc_metrics()suggest_rna_qc_thresholds()
- scranpy.run_all_neighbor_steps module
RunAllNeighborStepsResultsRunAllNeighborStepsResults.__annotations__RunAllNeighborStepsResults.__dataclass_fields__RunAllNeighborStepsResults.__dataclass_params__RunAllNeighborStepsResults.__eq__()RunAllNeighborStepsResults.__hash__RunAllNeighborStepsResults.__match_args__RunAllNeighborStepsResults.__repr__()RunAllNeighborStepsResults.build_snn_graphRunAllNeighborStepsResults.cluster_graphRunAllNeighborStepsResults.run_tsneRunAllNeighborStepsResults.run_umap
run_all_neighbor_steps()
- scranpy.run_pca module
RunPcaResultsRunPcaResults.__annotations__RunPcaResults.__dataclass_fields__RunPcaResults.__dataclass_params__RunPcaResults.__eq__()RunPcaResults.__hash__RunPcaResults.__match_args__RunPcaResults.__repr__()RunPcaResults.blockRunPcaResults.centerRunPcaResults.componentsRunPcaResults.rotationRunPcaResults.scaleRunPcaResults.total_varianceRunPcaResults.variance_explained
run_pca()
- scranpy.run_tsne module
- scranpy.run_umap module
- scranpy.sanitize_size_factors module
- scranpy.scale_by_neighbors module
ScaleByNeighborsResultsScaleByNeighborsResults.__annotations__ScaleByNeighborsResults.__dataclass_fields__ScaleByNeighborsResults.__dataclass_params__ScaleByNeighborsResults.__eq__()ScaleByNeighborsResults.__hash__ScaleByNeighborsResults.__match_args__ScaleByNeighborsResults.__repr__()ScaleByNeighborsResults.combinedScaleByNeighborsResults.scaling
scale_by_neighbors()
- scranpy.score_gene_set module
- scranpy.score_markers module
ScoreMarkersResultsScoreMarkersResults.__annotations__ScoreMarkersResults.__dataclass_fields__ScoreMarkersResults.__dataclass_params__ScoreMarkersResults.__eq__()ScoreMarkersResults.__hash__ScoreMarkersResults.__match_args__ScoreMarkersResults.__repr__()ScoreMarkersResults.aucScoreMarkersResults.cohens_dScoreMarkersResults.delta_detectedScoreMarkersResults.delta_meanScoreMarkersResults.detectedScoreMarkersResults.groupsScoreMarkersResults.meanScoreMarkersResults.to_biocframes()
score_markers()
- scranpy.subsample_by_neighbors module
- scranpy.summarize_effects module
GroupwiseSummarizedEffectsGroupwiseSummarizedEffects.__annotations__GroupwiseSummarizedEffects.__dataclass_fields__GroupwiseSummarizedEffects.__dataclass_params__GroupwiseSummarizedEffects.__eq__()GroupwiseSummarizedEffects.__hash__GroupwiseSummarizedEffects.__match_args__GroupwiseSummarizedEffects.__repr__()GroupwiseSummarizedEffects.maxGroupwiseSummarizedEffects.meanGroupwiseSummarizedEffects.medianGroupwiseSummarizedEffects.minGroupwiseSummarizedEffects.min_rankGroupwiseSummarizedEffects.to_biocframe()
summarize_effects()
- scranpy.test_enrichment module
- Module contents