Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | P | Q | R | S | T | U | V | W | X | Y _ __call__() (maldiamrkit.filters.DrugFilter method) (maldiamrkit.filters.MetadataFilter method) (maldiamrkit.filters.QualityFilter method) (maldiamrkit.filters.SpeciesFilter method) (maldiamrkit.filters.SpectrumFilter method) (maldiamrkit.preprocessing.ClipNegatives method) (maldiamrkit.preprocessing.ConvexHullBaseline method) (maldiamrkit.preprocessing.LogTransform method) (maldiamrkit.preprocessing.MedianBaseline method) (maldiamrkit.preprocessing.MedianNormalizer method) (maldiamrkit.preprocessing.MovingAverageSmooth method) (maldiamrkit.preprocessing.MzMultiTrimmer method) (maldiamrkit.preprocessing.MzTrimmer method) (maldiamrkit.preprocessing.PQNNormalizer method) (maldiamrkit.preprocessing.PreprocessingPipeline method) (maldiamrkit.preprocessing.SavitzkyGolaySmooth method) (maldiamrkit.preprocessing.SNIPBaseline method) (maldiamrkit.preprocessing.SqrtTransform method) (maldiamrkit.preprocessing.TICNormalizer method) (maldiamrkit.preprocessing.TopHatBaseline method) __init__() (maldiamrkit.alignment.RawWarping method) (maldiamrkit.alignment.Warping method) (maldiamrkit.data.BrukerTreeLayout method) (maldiamrkit.data.BuildReport method) (maldiamrkit.data.DatasetBuilder method) (maldiamrkit.data.DatasetLoader method) (maldiamrkit.data.DRIAMSLayout method) (maldiamrkit.data.FlatLayout method) (maldiamrkit.data.MARISMaLayout method) (maldiamrkit.data.ProcessingHandler method) (maldiamrkit.detection.MaldiPeakDetector method) (maldiamrkit.differential.DifferentialAnalysis method) (maldiamrkit.drift.DriftMonitor method) (maldiamrkit.evaluation.CaseGroupedKFold method) (maldiamrkit.evaluation.SpeciesDrugStratifiedKFold method) (maldiamrkit.filters.DrugFilter method) (maldiamrkit.filters.MetadataFilter method) (maldiamrkit.filters.QualityFilter method) (maldiamrkit.filters.SpeciesFilter method) (maldiamrkit.MaldiSet method) (maldiamrkit.MaldiSpectrum method) (maldiamrkit.preprocessing.MedianBaseline method) (maldiamrkit.preprocessing.MovingAverageSmooth method) (maldiamrkit.preprocessing.MzMultiTrimmer method) (maldiamrkit.preprocessing.MzTrimmer method) (maldiamrkit.preprocessing.PQNNormalizer method) (maldiamrkit.preprocessing.PreprocessingPipeline method) (maldiamrkit.preprocessing.SavitzkyGolaySmooth method) (maldiamrkit.preprocessing.SNIPBaseline method) (maldiamrkit.preprocessing.SpectrumQuality method) (maldiamrkit.preprocessing.SpectrumQualityReport method) (maldiamrkit.preprocessing.TopHatBaseline method) (maldiamrkit.susceptibility.BreakpointResult method) (maldiamrkit.susceptibility.BreakpointTable method) (maldiamrkit.susceptibility.LabelEncoder method) (maldiamrkit.susceptibility.MICEncoder method) A adaptive (maldiamrkit.preprocessing.BinningMethod attribute) align_binned() (maldiamrkit.alignment.AlignmentStrategy method) align_raw() (maldiamrkit.alignment.AlignmentStrategy method) AlignmentMethod (class in maldiamrkit.alignment) AlignmentStrategy (class in maldiamrkit.alignment) amr_classification_report() (in module maldiamrkit.evaluation) amr_multilabel_report() (in module maldiamrkit.evaluation) apply() (maldiamrkit.susceptibility.BreakpointTable method) apply_batch() (maldiamrkit.susceptibility.BreakpointTable method) assess() (maldiamrkit.preprocessing.SpectrumQuality method) atu (maldiamrkit.susceptibility.BreakpointResult attribute) average (maldiamrkit.data.DuplicateStrategy attribute) B baseline_end_ (maldiamrkit.drift.DriftMonitor property) bin() (maldiamrkit.MaldiSpectrum method) bin_metadata (maldiamrkit.MaldiSet property) (maldiamrkit.MaldiSpectrum property) bin_method (maldiamrkit.MaldiSpectrum property) bin_spectrum() (in module maldiamrkit.preprocessing) bin_width (maldiamrkit.data.ProcessingHandler attribute) (maldiamrkit.MaldiSpectrum property) binned (maldiamrkit.MaldiSpectrum property) BinningMethod (class in maldiamrkit.preprocessing) bonferroni (maldiamrkit.differential.CorrectionMethod attribute) BreakpointResult (class in maldiamrkit.susceptibility) BreakpointTable (class in maldiamrkit.susceptibility) BrukerTreeLayout (class in maldiamrkit.data) build (maldiamrkit.similarity.KMedoidsInit attribute) build() (maldiamrkit.data.DatasetBuilder method) BuildReport (class in maldiamrkit.data) C case_based_split() (in module maldiamrkit.evaluation) CaseGroupedKFold (class in maldiamrkit.evaluation) categorical_agreement() (in module maldiamrkit.evaluation) category (maldiamrkit.susceptibility.BreakpointResult attribute) ClipNegatives (class in maldiamrkit.preprocessing) cluster_metadata_concordance() (in module maldiamrkit.similarity) cluster_spectra() (in module maldiamrkit.similarity) ClusteringMethod (class in maldiamrkit.similarity) collect_spectrum_files() (maldiamrkit.data.DatasetLayout method) (maldiamrkit.data.DRIAMSLayout method) (maldiamrkit.data.MARISMaLayout method) compare_drugs() (maldiamrkit.differential.DifferentialAnalysis static method) ConvexHullBaseline (class in maldiamrkit.preprocessing) CorrectionMethod (class in maldiamrkit.differential) cosine (maldiamrkit.similarity.SpectralMetric attribute) count_peaks() (maldiamrkit.preprocessing.SpectrumQuality method) create_raw_input() (in module maldiamrkit.alignment) cubic (maldiamrkit.alignment.AlignmentMethod attribute) custom (maldiamrkit.preprocessing.BinningMethod attribute) D DatasetBuilder (class in maldiamrkit.data) DatasetLayout (class in maldiamrkit.data) DatasetLoader (class in maldiamrkit.data) default() (maldiamrkit.preprocessing.PreprocessingPipeline class method) detect_outlier_replicates() (in module maldiamrkit.preprocessing) detect_stage() (maldiamrkit.data.DatasetLayout method) (maldiamrkit.data.DRIAMSLayout method) (maldiamrkit.data.MARISMaLayout method) DifferentialAnalysis (class in maldiamrkit.differential) discover_metadata() (maldiamrkit.data.BrukerTreeLayout method) (maldiamrkit.data.DatasetLayout method) (maldiamrkit.data.DRIAMSLayout method) (maldiamrkit.data.FlatLayout method) (maldiamrkit.data.InputLayout method) (maldiamrkit.data.MARISMaLayout method) discover_spectra() (maldiamrkit.data.BrukerTreeLayout method) (maldiamrkit.data.FlatLayout method) (maldiamrkit.data.InputLayout method) DRIAMSLayout (class in maldiamrkit.data) DriftMonitor (class in maldiamrkit.drift) drop (maldiamrkit.data.DuplicateStrategy attribute) (maldiamrkit.susceptibility.IntermediateHandling attribute) DrugComparisonKind (class in maldiamrkit.differential) DrugFilter (class in maldiamrkit.filters) drugs() (maldiamrkit.susceptibility.BreakpointTable method) dtw (maldiamrkit.alignment.AlignmentMethod attribute) (maldiamrkit.similarity.SpectralMetric attribute) DuplicateStrategy (class in maldiamrkit.data) E estimate_baseline_fraction() (maldiamrkit.preprocessing.SpectrumQuality method) estimate_dynamic_range() (maldiamrkit.preprocessing.SpectrumQuality method) estimate_mad_noise() (maldiamrkit.preprocessing.SpectrumQuality method) estimate_noise_level() (maldiamrkit.preprocessing.SpectrumQuality method) estimate_snr() (in module maldiamrkit.preprocessing) F fdr_bh (maldiamrkit.differential.CorrectionMethod attribute) fdr_by (maldiamrkit.differential.CorrectionMethod attribute) filter() (maldiamrkit.MaldiSet method) first (maldiamrkit.data.DuplicateStrategy attribute) fit() (maldiamrkit.alignment.RawWarping method) (maldiamrkit.alignment.Warping method) (maldiamrkit.detection.MaldiPeakDetector method) (maldiamrkit.drift.DriftMonitor method) (maldiamrkit.susceptibility.LabelEncoder method) (maldiamrkit.susceptibility.MICEncoder method) fit_transform() (maldiamrkit.detection.MaldiPeakDetector method) (maldiamrkit.susceptibility.LabelEncoder method) (maldiamrkit.susceptibility.MICEncoder method) FlatLayout (class in maldiamrkit.data) folder_name (maldiamrkit.data.ProcessingHandler attribute) from_dict() (maldiamrkit.data.ProcessingHandler class method) (maldiamrkit.preprocessing.PreprocessingPipeline class method) from_directory() (maldiamrkit.MaldiSet class method) from_json() (maldiamrkit.preprocessing.PreprocessingPipeline class method) from_latest() (maldiamrkit.susceptibility.BreakpointTable class method) from_maldi_set() (maldiamrkit.differential.DifferentialAnalysis class method) from_version() (maldiamrkit.susceptibility.BreakpointTable class method) from_yaml() (maldiamrkit.preprocessing.PreprocessingPipeline class method) (maldiamrkit.susceptibility.BreakpointTable class method) from_year() (maldiamrkit.susceptibility.BreakpointTable class method) G get_alignment_quality() (maldiamrkit.alignment.RawWarping method) (maldiamrkit.alignment.Warping method) get_bin_metadata() (in module maldiamrkit.preprocessing) get_data() (maldiamrkit.MaldiSpectrum method) get_feature_names_out() (maldiamrkit.susceptibility.MICEncoder method) get_id() (maldiamrkit.data.BrukerTreeLayout method) (maldiamrkit.data.FlatLayout method) (maldiamrkit.data.InputLayout method) get_n_splits() (maldiamrkit.evaluation.CaseGroupedKFold method) (maldiamrkit.evaluation.SpeciesDrugStratifiedKFold method) get_peak_statistics() (maldiamrkit.detection.MaldiPeakDetector method) get_step() (maldiamrkit.preprocessing.PreprocessingPipeline method) get_y_single() (maldiamrkit.MaldiSet method) get_year() (maldiamrkit.data.BrukerTreeLayout method) (maldiamrkit.data.FlatLayout method) (maldiamrkit.data.InputLayout method) H has_bin_metadata (maldiamrkit.MaldiSpectrum property) hdbscan (maldiamrkit.similarity.ClusteringMethod attribute) hdbscan_clustering() (in module maldiamrkit.similarity) heatmap (maldiamrkit.differential.DrugComparisonKind attribute) hierarchical (maldiamrkit.similarity.ClusteringMethod attribute) hierarchical_clustering() (in module maldiamrkit.similarity) I InputLayout (class in maldiamrkit.data) IntermediateHandling (class in maldiamrkit.susceptibility) is_binned (maldiamrkit.MaldiSpectrum property) is_preprocessed (maldiamrkit.MaldiSpectrum property) K keep_all (maldiamrkit.data.DuplicateStrategy attribute) kind (maldiamrkit.data.ProcessingHandler attribute) kmedoids (maldiamrkit.similarity.ClusteringMethod attribute) kmedoids_clustering() (in module maldiamrkit.similarity) KMedoidsInit (class in maldiamrkit.similarity) L LabelEncoder (class in maldiamrkit.susceptibility) last (maldiamrkit.data.DuplicateStrategy attribute) linear (maldiamrkit.alignment.AlignmentMethod attribute) list_available() (maldiamrkit.susceptibility.BreakpointTable class method) load() (maldiamrkit.data.DatasetLoader method) local (maldiamrkit.detection.PeakMethod attribute) LogTransform (class in maldiamrkit.preprocessing) lowess (maldiamrkit.alignment.AlignmentMethod attribute) M major_error_rate() (in module maldiamrkit.evaluation) maldiamrkit.evaluation module maldiamrkit.evaluation.me_scorer (in module maldiamrkit.evaluation) maldiamrkit.evaluation.vme_scorer (in module maldiamrkit.evaluation) maldiamrkit.similarity.METRIC_REGISTRY (built-in variable) maldiamrkit.susceptibility module MaldiPeakDetector (class in maldiamrkit.detection) MaldiSet (class in maldiamrkit) MaldiSpectrum (class in maldiamrkit) mann_whitney (maldiamrkit.differential.StatisticalTest attribute) MARISMaLayout (class in maldiamrkit.data) max (maldiamrkit.preprocessing.SignalMethod attribute) mean (maldiamrkit.preprocessing.MergingMethod attribute) median (maldiamrkit.preprocessing.MergingMethod attribute) median_peaks (maldiamrkit.preprocessing.SignalMethod attribute) MedianBaseline (class in maldiamrkit.preprocessing) MedianNormalizer (class in maldiamrkit.preprocessing) merge_replicates() (in module maldiamrkit.preprocessing) MergingMethod (class in maldiamrkit.preprocessing) MetadataFilter (class in maldiamrkit.filters) mic_regression_report() (in module maldiamrkit.evaluation) MICEncoder (class in maldiamrkit.susceptibility) module maldiamrkit.evaluation maldiamrkit.susceptibility monitor() (maldiamrkit.drift.DriftMonitor method) monitor_effect_sizes() (maldiamrkit.drift.DriftMonitor method) monitor_pca() (maldiamrkit.drift.DriftMonitor method) monitor_peak_stability() (maldiamrkit.drift.DriftMonitor method) MovingAverageSmooth (class in maldiamrkit.preprocessing) mz_range (maldiamrkit.preprocessing.PreprocessingPipeline property) MzMultiTrimmer (class in maldiamrkit.preprocessing) MzTrimmer (class in maldiamrkit.preprocessing) N nan (maldiamrkit.susceptibility.IntermediateHandling attribute) P pairwise_distances() (in module maldiamrkit.similarity) parse_mic_column() (in module maldiamrkit.io) PeakMethod (class in maldiamrkit.detection) pearson (maldiamrkit.similarity.SpectralMetric attribute) ph (maldiamrkit.detection.PeakMethod attribute) piecewise (maldiamrkit.alignment.AlignmentMethod attribute) pipeline (maldiamrkit.data.ProcessingHandler attribute) plot_alignment() (in module maldiamrkit.visualization) plot_dendrogram() (in module maldiamrkit.similarity) plot_distance_heatmap() (in module maldiamrkit.similarity) plot_drug_comparison() (in module maldiamrkit.differential) plot_effect_size_drift() (in module maldiamrkit.drift) plot_manhattan() (in module maldiamrkit.differential) plot_pca() (in module maldiamrkit.visualization) plot_pca_drift() (in module maldiamrkit.drift) plot_peak_stability() (in module maldiamrkit.drift) plot_peaks() (in module maldiamrkit.visualization) plot_pseudogel() (in module maldiamrkit.visualization) plot_reference_drift() (in module maldiamrkit.drift) plot_spectrum() (in module maldiamrkit.visualization) plot_tsne() (in module maldiamrkit.visualization) plot_umap() (in module maldiamrkit.visualization) plot_volcano() (in module maldiamrkit.differential) postprocess_spectrum() (maldiamrkit.data.DatasetLayout method) (maldiamrkit.data.DRIAMSLayout method) PQNNormalizer (class in maldiamrkit.preprocessing) preprocess() (in module maldiamrkit.preprocessing) (maldiamrkit.MaldiSpectrum method) preprocessed (maldiamrkit.MaldiSpectrum property) PreprocessingPipeline (class in maldiamrkit.preprocessing) ProcessingHandler (class in maldiamrkit.data) proportional (maldiamrkit.preprocessing.BinningMethod attribute) Q quadratic (maldiamrkit.alignment.AlignmentMethod attribute) QualityFilter (class in maldiamrkit.filters) R random (maldiamrkit.similarity.KMedoidsInit attribute) raw (maldiamrkit.MaldiSpectrum property) RawWarping (class in maldiamrkit.alignment) read_spectrum() (in module maldiamrkit.io) reference_ (maldiamrkit.drift.DriftMonitor property) resistant (maldiamrkit.susceptibility.IntermediateHandling attribute) results (maldiamrkit.differential.DifferentialAnalysis property) rows (maldiamrkit.susceptibility.BreakpointTable property) run() (maldiamrkit.differential.DifferentialAnalysis method) S save() (maldiamrkit.MaldiSpectrum method) save_spectra() (maldiamrkit.MaldiSet method) SavitzkyGolaySmooth (class in maldiamrkit.preprocessing) sensitivity_score() (in module maldiamrkit.evaluation) shift (maldiamrkit.alignment.AlignmentMethod attribute) SignalMethod (class in maldiamrkit.preprocessing) significant_peaks() (maldiamrkit.differential.DifferentialAnalysis method) silhouette_scores() (in module maldiamrkit.similarity) SNIPBaseline (class in maldiamrkit.preprocessing) source (maldiamrkit.susceptibility.BreakpointResult attribute) species() (maldiamrkit.susceptibility.BreakpointTable method) SpeciesDrugStratifiedKFold (class in maldiamrkit.evaluation) SpeciesFilter (class in maldiamrkit.filters) specificity_score() (in module maldiamrkit.evaluation) spectra_paths (maldiamrkit.MaldiSet property) spectral_contrast_angle (maldiamrkit.similarity.SpectralMetric attribute) spectral_distance() (in module maldiamrkit.similarity) SpectralMetric (class in maldiamrkit.similarity) SpectrumFilter (class in maldiamrkit.filters) SpectrumQuality (class in maldiamrkit.preprocessing) SpectrumQualityReport (class in maldiamrkit.preprocessing) split() (maldiamrkit.evaluation.CaseGroupedKFold method) (maldiamrkit.evaluation.SpeciesDrugStratifiedKFold method) SqrtTransform (class in maldiamrkit.preprocessing) StatisticalTest (class in maldiamrkit.differential) step_names (maldiamrkit.preprocessing.PreprocessingPipeline property) stratified_species_drug_split() (in module maldiamrkit.evaluation) susceptible (maldiamrkit.susceptibility.IntermediateHandling attribute) T t_test (maldiamrkit.differential.StatisticalTest attribute) TICNormalizer (class in maldiamrkit.preprocessing) to_csv() (maldiamrkit.MaldiSet method) to_dict() (maldiamrkit.data.ProcessingHandler method) (maldiamrkit.preprocessing.ClipNegatives method) (maldiamrkit.preprocessing.ConvexHullBaseline method) (maldiamrkit.preprocessing.LogTransform method) (maldiamrkit.preprocessing.MedianBaseline method) (maldiamrkit.preprocessing.MedianNormalizer method) (maldiamrkit.preprocessing.MovingAverageSmooth method) (maldiamrkit.preprocessing.MzMultiTrimmer method) (maldiamrkit.preprocessing.MzTrimmer method) (maldiamrkit.preprocessing.PQNNormalizer method) (maldiamrkit.preprocessing.PreprocessingPipeline method) (maldiamrkit.preprocessing.SavitzkyGolaySmooth method) (maldiamrkit.preprocessing.SNIPBaseline method) (maldiamrkit.preprocessing.SqrtTransform method) (maldiamrkit.preprocessing.TICNormalizer method) (maldiamrkit.preprocessing.TopHatBaseline method) to_json() (maldiamrkit.preprocessing.PreprocessingPipeline method) to_parquet() (maldiamrkit.MaldiSet method) to_yaml() (maldiamrkit.preprocessing.PreprocessingPipeline method) top_peaks() (maldiamrkit.differential.DifferentialAnalysis method) TopHatBaseline (class in maldiamrkit.preprocessing) transform() (maldiamrkit.alignment.RawWarping method) (maldiamrkit.alignment.Warping method) (maldiamrkit.detection.MaldiPeakDetector method) (maldiamrkit.susceptibility.LabelEncoder method) (maldiamrkit.susceptibility.MICEncoder method) U uniform (maldiamrkit.preprocessing.BinningMethod attribute) upset (maldiamrkit.differential.DrugComparisonKind attribute) V very_major_error_rate() (in module maldiamrkit.evaluation) vme_me_curve() (in module maldiamrkit.evaluation) W Warping (class in maldiamrkit.alignment) wasserstein (maldiamrkit.similarity.SpectralMetric attribute) X X (maldiamrkit.MaldiSet property) Y y (maldiamrkit.MaldiSet property)
