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CytoNormPy
Installation
CytoNormPy Public API
CytoNorm
cytonormpy.CytoNorm
cytonormpy.CytoNorm.add_clusterer
cytonormpy.CytoNorm.add_transformer
cytonormpy.CytoNorm.calculate_cluster_cvs
cytonormpy.CytoNorm.calculate_emd
cytonormpy.CytoNorm.calculate_mad
cytonormpy.CytoNorm.calculate_quantiles
cytonormpy.CytoNorm.calculate_splines
cytonormpy.CytoNorm.normalize_data
cytonormpy.CytoNorm.run_anndata_setup
cytonormpy.CytoNorm.run_clustering
cytonormpy.CytoNorm.run_fcs_data_setup
cytonormpy.CytoNorm.save_model
Plotting utilities
cytonormpy.pl.scatter
cytonormpy.pl.histogram
cytonormpy.pl.cv_heatmap
cytonormpy.pl.emd
cytonormpy.pl.mad
cytonormpy.pl.splineplot
Clustering utilities
cytonormpy.FlowSOM
cytonormpy.FlowSOM.calculate_clusters
cytonormpy.FlowSOM.calculate_clusters_multiple
cytonormpy.FlowSOM.train
cytonormpy.KMeans
cytonormpy.KMeans.calculate_clusters
cytonormpy.KMeans.calculate_clusters_multiple
cytonormpy.KMeans.train
cytonormpy.MeanShift
cytonormpy.MeanShift.calculate_clusters
cytonormpy.MeanShift.calculate_clusters_multiple
cytonormpy.MeanShift.train
cytonormpy.AffinityPropagation
cytonormpy.AffinityPropagation.calculate_clusters
cytonormpy.AffinityPropagation.calculate_clusters_multiple
cytonormpy.AffinityPropagation.train
Transformation utilities
cytonormpy.AsinhTransformer
cytonormpy.AsinhTransformer.channel_indices
cytonormpy.AsinhTransformer.inverse_transform
cytonormpy.AsinhTransformer.transform
cytonormpy.LogTransformer
cytonormpy.LogTransformer.channel_indices
cytonormpy.LogTransformer.inverse_transform
cytonormpy.LogTransformer.transform
cytonormpy.LogicleTransformer
cytonormpy.LogicleTransformer.channel_indices
cytonormpy.LogicleTransformer.inverse_transform
cytonormpy.LogicleTransformer.transform
cytonormpy.HyperLogTransformer
cytonormpy.HyperLogTransformer.channel_indices
cytonormpy.HyperLogTransformer.inverse_transform
cytonormpy.HyperLogTransformer.transform
Other functions
cytonormpy.read_model
cytonormpy.mad_from_fcs
cytonormpy.mad_comparison_from_fcs
cytonormpy.mad_from_anndata
cytonormpy.mad_comparison_from_anndata
cytonormpy.emd_from_fcs
cytonormpy.emd_comparison_from_fcs
cytonormpy.emd_from_anndata
cytonormpy.emd_comparison_from_anndata
CytoNormPy Private API
Splines
cytonormpy._normalization.IdentitySpline
cytonormpy._normalization.Spline
cytonormpy._normalization.Spline.fit
cytonormpy._normalization.Spline.is_fit
cytonormpy._normalization.Spline.transform
cytonormpy._normalization.Splines
cytonormpy._normalization.Splines.add_spline
cytonormpy._normalization.Splines.get_spline
cytonormpy._normalization.Splines.remove_spline
cytonormpy._normalization.Splines.transform
Quantiles
cytonormpy._normalization.ExpressionQuantiles
cytonormpy._normalization.ExpressionQuantiles.add_nan_slice
cytonormpy._normalization.ExpressionQuantiles.add_quantiles
cytonormpy._normalization.ExpressionQuantiles.calculate_and_add_quantiles
cytonormpy._normalization.ExpressionQuantiles.calculate_quantiles
cytonormpy._normalization.ExpressionQuantiles.get_quantiles
cytonormpy._normalization.GoalDistribution
cytonormpy._normalization.GoalDistribution.get_quantiles
Data Handlers
cytonormpy._dataset.DataHandlerFCS
cytonormpy._dataset.DataHandlerFCS.cytof_technicals
cytonormpy._dataset.DataHandlerFCS.flow_technicals
cytonormpy._dataset.DataHandlerFCS.spectral_flow_technicals
cytonormpy._dataset.DataHandlerFCS.metadata
cytonormpy._dataset.DataHandlerFCS.n_cells_reference
cytonormpy._dataset.DataHandlerFCS.add_file
cytonormpy._dataset.DataHandlerFCS.append_cytof_technicals
cytonormpy._dataset.DataHandlerFCS.append_flow_technicals
cytonormpy._dataset.DataHandlerFCS.append_spectral_flow_technicals
cytonormpy._dataset.DataHandlerFCS.get_corresponding_ref_dataframe
cytonormpy._dataset.DataHandlerFCS.get_dataframe
cytonormpy._dataset.DataHandlerFCS.get_ref_data_df
cytonormpy._dataset.DataHandlerFCS.get_ref_data_df_subsampled
cytonormpy._dataset.DataHandlerFCS.write
cytonormpy._dataset.DataHandlerAnnData
cytonormpy._dataset.DataHandlerAnnData.cytof_technicals
cytonormpy._dataset.DataHandlerAnnData.flow_technicals
cytonormpy._dataset.DataHandlerAnnData.spectral_flow_technicals
cytonormpy._dataset.DataHandlerAnnData.metadata
cytonormpy._dataset.DataHandlerAnnData.n_cells_reference
cytonormpy._dataset.DataHandlerAnnData.add_file
cytonormpy._dataset.DataHandlerAnnData.append_cytof_technicals
cytonormpy._dataset.DataHandlerAnnData.append_flow_technicals
cytonormpy._dataset.DataHandlerAnnData.append_spectral_flow_technicals
cytonormpy._dataset.DataHandlerAnnData.get_corresponding_ref_dataframe
cytonormpy._dataset.DataHandlerAnnData.get_dataframe
cytonormpy._dataset.DataHandlerAnnData.get_ref_data_df
cytonormpy._dataset.DataHandlerAnnData.get_ref_data_df_subsampled
cytonormpy._dataset.DataHandlerAnnData.write
cytonormpy._dataset.FCSFile
cytonormpy._dataset.FCSFile.get_channel_index
cytonormpy._dataset.FCSFile.get_events
cytonormpy._dataset.FCSFile.to_df
Data Providers
cytonormpy._dataset.DataProvider
cytonormpy._dataset.DataProvider.channels
cytonormpy._dataset.DataProvider.transformer
cytonormpy._dataset.DataProvider.annotate_metadata
cytonormpy._dataset.DataProvider.annotate_metadata_old
cytonormpy._dataset.DataProvider.inverse_transform_data
cytonormpy._dataset.DataProvider.parse_raw_data
cytonormpy._dataset.DataProvider.prep_dataframe
cytonormpy._dataset.DataProvider.select_channels
cytonormpy._dataset.DataProvider.subsample_df
cytonormpy._dataset.DataProvider.transform_data
cytonormpy._dataset.DataProviderFCS
cytonormpy._dataset.DataProviderFCS.channels
cytonormpy._dataset.DataProviderFCS.transformer
cytonormpy._dataset.DataProviderFCS.annotate_metadata
cytonormpy._dataset.DataProviderFCS.annotate_metadata_old
cytonormpy._dataset.DataProviderFCS.inverse_transform_data
cytonormpy._dataset.DataProviderFCS.parse_raw_data
cytonormpy._dataset.DataProviderFCS.prep_dataframe
cytonormpy._dataset.DataProviderFCS.select_channels
cytonormpy._dataset.DataProviderFCS.subsample_df
cytonormpy._dataset.DataProviderFCS.transform_data
cytonormpy._dataset.DataProviderAnnData
cytonormpy._dataset.DataProviderAnnData.channels
cytonormpy._dataset.DataProviderAnnData.transformer
cytonormpy._dataset.DataProviderAnnData.annotate_metadata
cytonormpy._dataset.DataProviderAnnData.annotate_metadata_old
cytonormpy._dataset.DataProviderAnnData.inverse_transform_data
cytonormpy._dataset.DataProviderAnnData.parse_raw_data
cytonormpy._dataset.DataProviderAnnData.prep_dataframe
cytonormpy._dataset.DataProviderAnnData.select_channels
cytonormpy._dataset.DataProviderAnnData.subsample_df
cytonormpy._dataset.DataProviderAnnData.transform_data
Metadata
cytonormpy._dataset.Metadata
cytonormpy._dataset.Metadata.add_file_to_metadata
cytonormpy._dataset.Metadata.assemble_reference_assembly_dict
cytonormpy._dataset.Metadata.convert_batch_dtype
cytonormpy._dataset.Metadata.find_batches_without_reference
cytonormpy._dataset.Metadata.get_batch
cytonormpy._dataset.Metadata.get_corresponding_reference_file
cytonormpy._dataset.Metadata.get_files_per_batch
cytonormpy._dataset.Metadata.get_ref_value
cytonormpy._dataset.Metadata.get_reference_file_names
cytonormpy._dataset.Metadata.get_validation_file_names
cytonormpy._dataset.Metadata.to_df
cytonormpy._dataset.Metadata.update
cytonormpy._dataset.Metadata.validate_batch_references
cytonormpy._dataset.Metadata.validate_metadata
cytonormpy._dataset.Metadata.validate_metadata_table
Warnings
cytonormpy._cytonorm._cytonorm.ClusterCVWarning
cytonormpy._dataset._fcs_file.NaNRemovalWarning
cytonormpy._dataset._fcs_file.TruncationWarning
cytonormpy._dataset._fcs_file.InfRemovalWarning
Vignettes
CytoNormPy - AnnData objects
CytoNormPy - FCS files
CytoNormPy - Plotting
References
.md
.pdf
CytoNorm
CytoNorm
#
CytoNorm
Cytometry data are divided into batches.