Index A | C | D | E | F | G | H | I | K | L | M | N | P | R | S | T | U | V | W A add_clusterer() (cytonormpy.CytoNorm method) add_file() (cytonormpy._dataset.DataHandlerAnnData method) (cytonormpy._dataset.DataHandlerFCS method) add_file_to_metadata() (cytonormpy._dataset.Metadata method) add_nan_slice() (cytonormpy._normalization.ExpressionQuantiles method) add_quantiles() (cytonormpy._normalization.ExpressionQuantiles method) add_spline() (cytonormpy._normalization.Splines method) add_transformer() (cytonormpy.CytoNorm method) AffinityPropagation (class in cytonormpy) annotate_metadata() (cytonormpy._dataset.DataProvider method) (cytonormpy._dataset.DataProviderAnnData method) (cytonormpy._dataset.DataProviderFCS method) annotate_metadata_old() (cytonormpy._dataset.DataProvider method) (cytonormpy._dataset.DataProviderAnnData method) (cytonormpy._dataset.DataProviderFCS method) append_cytof_technicals() (cytonormpy._dataset.DataHandlerAnnData method) (cytonormpy._dataset.DataHandlerFCS method) append_flow_technicals() (cytonormpy._dataset.DataHandlerAnnData method) (cytonormpy._dataset.DataHandlerFCS method) append_spectral_flow_technicals() (cytonormpy._dataset.DataHandlerAnnData method) (cytonormpy._dataset.DataHandlerFCS method) AsinhTransformer (class in cytonormpy) assemble_reference_assembly_dict() (cytonormpy._dataset.Metadata method) C calculate_and_add_quantiles() (cytonormpy._normalization.ExpressionQuantiles method) calculate_cluster_cvs() (cytonormpy.CytoNorm method) calculate_clusters() (cytonormpy.AffinityPropagation method) (cytonormpy.FlowSOM method) (cytonormpy.KMeans method) (cytonormpy.MeanShift method) calculate_clusters_multiple() (cytonormpy.AffinityPropagation method) (cytonormpy.FlowSOM method) (cytonormpy.KMeans method) (cytonormpy.MeanShift method) calculate_emd() (cytonormpy.CytoNorm method) calculate_mad() (cytonormpy.CytoNorm method) calculate_quantiles() (cytonormpy._normalization.ExpressionQuantiles method) (cytonormpy.CytoNorm method) calculate_splines() (cytonormpy.CytoNorm method) channel_indices (cytonormpy.AsinhTransformer property) (cytonormpy.HyperLogTransformer property) (cytonormpy.LogicleTransformer property) (cytonormpy.LogTransformer property) channels (cytonormpy._dataset.DataProvider property) (cytonormpy._dataset.DataProviderAnnData property) (cytonormpy._dataset.DataProviderFCS property) ClusterCVWarning convert_batch_dtype() (cytonormpy._dataset.Metadata method) cv_heatmap() (in module cytonormpy.pl) cvs_by_k (cytonormpy.CytoNorm attribute) cytof_technicals (cytonormpy._dataset.DataHandlerAnnData property) (cytonormpy._dataset.DataHandlerFCS property) CytoNorm (class in cytonormpy) cytonormpy module cytonormpy._normalization module D DataHandlerAnnData (class in cytonormpy._dataset) DataHandlerFCS (class in cytonormpy._dataset) DataProvider (class in cytonormpy._dataset) DataProviderAnnData (class in cytonormpy._dataset) DataProviderFCS (class in cytonormpy._dataset) E emd() (in module cytonormpy.pl) emd_comparison_from_anndata() (in module cytonormpy) emd_comparison_from_fcs() (in module cytonormpy) emd_from_anndata() (in module cytonormpy) emd_from_fcs() (in module cytonormpy) ExpressionQuantiles (class in cytonormpy._normalization) F FCSFile (class in cytonormpy._dataset) find_batches_without_reference() (cytonormpy._dataset.Metadata method) fit() (cytonormpy._normalization.Spline method) flow_technicals (cytonormpy._dataset.DataHandlerAnnData property) (cytonormpy._dataset.DataHandlerFCS property) FlowSOM (class in cytonormpy) G get_batch() (cytonormpy._dataset.Metadata method) get_channel_index() (cytonormpy._dataset.FCSFile method) get_corresponding_ref_dataframe() (cytonormpy._dataset.DataHandlerAnnData method) (cytonormpy._dataset.DataHandlerFCS method) get_corresponding_reference_file() (cytonormpy._dataset.Metadata method) get_dataframe() (cytonormpy._dataset.DataHandlerAnnData method) (cytonormpy._dataset.DataHandlerFCS method) get_events() (cytonormpy._dataset.FCSFile method) get_files_per_batch() (cytonormpy._dataset.Metadata method) get_quantiles() (cytonormpy._normalization.ExpressionQuantiles method) (cytonormpy._normalization.GoalDistribution method) get_ref_data_df() (cytonormpy._dataset.DataHandlerAnnData method) (cytonormpy._dataset.DataHandlerFCS method) get_ref_data_df_subsampled() (cytonormpy._dataset.DataHandlerAnnData method) (cytonormpy._dataset.DataHandlerFCS method) get_ref_value() (cytonormpy._dataset.Metadata method) get_reference_file_names() (cytonormpy._dataset.Metadata method) get_spline() (cytonormpy._normalization.Splines method) get_validation_file_names() (cytonormpy._dataset.Metadata method) GoalDistribution (class in cytonormpy._normalization) H histogram() (in module cytonormpy.pl) HyperLogTransformer (class in cytonormpy) I IdentitySpline (class in cytonormpy._normalization) InfRemovalWarning inverse_transform() (cytonormpy.AsinhTransformer method) (cytonormpy.HyperLogTransformer method) (cytonormpy.LogicleTransformer method) (cytonormpy.LogTransformer method) inverse_transform_data() (cytonormpy._dataset.DataProvider method) (cytonormpy._dataset.DataProviderAnnData method) (cytonormpy._dataset.DataProviderFCS method) is_fit() (cytonormpy._normalization.Spline method) K KMeans (class in cytonormpy) L LogicleTransformer (class in cytonormpy) LogTransformer (class in cytonormpy) M mad() (in module cytonormpy.pl) mad_comparison_from_anndata() (in module cytonormpy) mad_comparison_from_fcs() (in module cytonormpy) mad_from_anndata() (in module cytonormpy) mad_from_fcs() (in module cytonormpy) MeanShift (class in cytonormpy) Metadata (class in cytonormpy._dataset) metadata (cytonormpy._dataset.DataHandlerAnnData attribute) (cytonormpy._dataset.DataHandlerFCS attribute) module cytonormpy cytonormpy._normalization N n_cells_reference (cytonormpy._dataset.DataHandlerAnnData attribute) (cytonormpy._dataset.DataHandlerFCS attribute) NaNRemovalWarning normalize_data() (cytonormpy.CytoNorm method) P parse_raw_data() (cytonormpy._dataset.DataProvider method) (cytonormpy._dataset.DataProviderAnnData method) (cytonormpy._dataset.DataProviderFCS method) prep_dataframe() (cytonormpy._dataset.DataProvider method) (cytonormpy._dataset.DataProviderAnnData method) (cytonormpy._dataset.DataProviderFCS method) R read_model() (in module cytonormpy) remove_spline() (cytonormpy._normalization.Splines method) run_anndata_setup() (cytonormpy.CytoNorm method) run_clustering() (cytonormpy.CytoNorm method) run_fcs_data_setup() (cytonormpy.CytoNorm method) S save_model() (cytonormpy.CytoNorm method) scatter() (in module cytonormpy.pl) select_channels() (cytonormpy._dataset.DataProvider method) (cytonormpy._dataset.DataProviderAnnData method) (cytonormpy._dataset.DataProviderFCS method) spectral_flow_technicals (cytonormpy._dataset.DataHandlerAnnData property) (cytonormpy._dataset.DataHandlerFCS property) Spline (class in cytonormpy._normalization) splineplot() (in module cytonormpy.pl) Splines (class in cytonormpy._normalization) subsample_df() (cytonormpy._dataset.DataProvider method) (cytonormpy._dataset.DataProviderAnnData method) (cytonormpy._dataset.DataProviderFCS method) T to_df() (cytonormpy._dataset.FCSFile method) (cytonormpy._dataset.Metadata method) train() (cytonormpy.AffinityPropagation method) (cytonormpy.FlowSOM method) (cytonormpy.KMeans method) (cytonormpy.MeanShift method) transform() (cytonormpy._normalization.Spline method) (cytonormpy._normalization.Splines method) (cytonormpy.AsinhTransformer method) (cytonormpy.HyperLogTransformer method) (cytonormpy.LogicleTransformer method) (cytonormpy.LogTransformer method) transform_data() (cytonormpy._dataset.DataProvider method) (cytonormpy._dataset.DataProviderAnnData method) (cytonormpy._dataset.DataProviderFCS method) transformer (cytonormpy._dataset.DataProvider property) (cytonormpy._dataset.DataProviderAnnData property) (cytonormpy._dataset.DataProviderFCS property) TruncationWarning U update() (cytonormpy._dataset.Metadata method) V validate_batch_references() (cytonormpy._dataset.Metadata method) validate_metadata() (cytonormpy._dataset.Metadata method) validate_metadata_table() (cytonormpy._dataset.Metadata method) W write() (cytonormpy._dataset.DataHandlerAnnData method) (cytonormpy._dataset.DataHandlerFCS method)