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.BuildInfo 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.data.SiteInfo method) (maldiamrkit.detection.MaldiPeakDetector method) (maldiamrkit.detection.PeakList method) (maldiamrkit.detection.PeakSet 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_peaks() (in module maldiamrkit.alignment) 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) as_array() (maldiamrkit.detection.PeakSet 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.data.SiteInfo 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) build_info (maldiamrkit.data.SiteInfo attribute) BuildInfo (class in maldiamrkit.data) 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_peakset_input() (in module maldiamrkit.detection) create_raw_input() (in module maldiamrkit.alignment) created_at (maldiamrkit.data.BuildInfo attribute) 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_peakset() (maldiamrkit.detection.MaldiPeakDetector method) 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) duplicate_strategy (maldiamrkit.data.BuildInfo 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) format_version (maldiamrkit.data.SiteInfo 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) groups (maldiamrkit.MaldiSet property) 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 id_column (maldiamrkit.data.SiteInfo attribute) index (maldiamrkit.detection.PeakList attribute) InputLayout (class in maldiamrkit.data) intensity (maldiamrkit.detection.PeakSet attribute) IntermediateHandling (class in maldiamrkit.susceptibility) is_binned (maldiamrkit.MaldiSpectrum property) is_preprocessed (maldiamrkit.MaldiSpectrum property) isolate_column (maldiamrkit.data.DatasetLayout attribute) isolate_ids() (maldiamrkit.MaldiSet method) 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) (maldiamrkit.detection.PeakList class 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.susceptibility module maldiamrkit_version (maldiamrkit.data.BuildInfo attribute) 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) meta (maldiamrkit.detection.PeakList attribute) metadata_dir (maldiamrkit.data.SiteInfo attribute) metadata_suffix (maldiamrkit.data.SiteInfo attribute) 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 (maldiamrkit.detection.PeakSet attribute) mz_range (maldiamrkit.data.SiteInfo attribute) (maldiamrkit.preprocessing.PreprocessingPipeline property) MzMultiTrimmer (class in maldiamrkit.preprocessing) MzTrimmer (class in maldiamrkit.preprocessing) N n_failed (maldiamrkit.data.BuildInfo attribute) n_peaks (maldiamrkit.detection.PeakList property) (maldiamrkit.detection.PeakSet property) n_succeeded (maldiamrkit.data.BuildInfo attribute) n_total_spectra (maldiamrkit.data.BuildInfo attribute) nan (maldiamrkit.susceptibility.IntermediateHandling attribute) P pairwise_distances() (in module maldiamrkit.similarity) parse_mic_column() (in module maldiamrkit.io) PeakList (class in maldiamrkit.detection) PeakMethod (class in maldiamrkit.detection) peaks (maldiamrkit.detection.PeakList attribute) PeakSet (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_site_info() (in module maldiamrkit.data) read_spectrum() (in module maldiamrkit.io) reference_ (maldiamrkit.drift.DriftMonitor property) register_binning_method() (in module maldiamrkit.preprocessing) replicate_pattern (maldiamrkit.data.DatasetLayout attribute) (maldiamrkit.data.DRIAMSLayout attribute) resistant (maldiamrkit.susceptibility.IntermediateHandling attribute) results (maldiamrkit.differential.DifferentialAnalysis property) rows (maldiamrkit.susceptibility.BreakpointTable property) run() (maldiamrkit.differential.DifferentialAnalysis method) S save() (maldiamrkit.detection.PeakList method) (maldiamrkit.MaldiSpectrum method) save_spectra() (maldiamrkit.MaldiSet method) SavitzkyGolaySmooth (class in maldiamrkit.preprocessing) score (maldiamrkit.detection.PeakSet attribute) 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) SiteInfo (class in maldiamrkit.data) SNIPBaseline (class in maldiamrkit.preprocessing) source (maldiamrkit.susceptibility.BreakpointResult attribute) source_layout (maldiamrkit.data.BuildInfo attribute) species() (maldiamrkit.susceptibility.BreakpointTable method) SpeciesDrugStratifiedKFold (class in maldiamrkit.evaluation) SpeciesFilter (class in maldiamrkit.filters) specificity_score() (in module maldiamrkit.evaluation) spectra_folders (maldiamrkit.data.SiteInfo attribute) spectra_paths (maldiamrkit.MaldiSet property) spectral_contrast_angle (maldiamrkit.similarity.SpectralMetric attribute) spectral_distance() (in module maldiamrkit.similarity) SpectralMetric (class in maldiamrkit.similarity) spectrum_ext (maldiamrkit.data.SiteInfo attribute) 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) strip_driams_replicate() (in module maldiamrkit.data) 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.BuildInfo method) (maldiamrkit.data.ProcessingHandler method) (maldiamrkit.data.SiteInfo 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_padded() (maldiamrkit.detection.PeakList method) to_parquet() (maldiamrkit.MaldiSet method) to_yaml() (maldiamrkit.preprocessing.PreprocessingPipeline method) top_k() (maldiamrkit.detection.PeakSet 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) transform_peaklist() (maldiamrkit.detection.MaldiPeakDetector method) U uniform (maldiamrkit.preprocessing.BinningMethod attribute) unregister_binning_method() (in module maldiamrkit.preprocessing) 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) write_site_info() (in module maldiamrkit.data) X X (maldiamrkit.MaldiSet property) Y y (maldiamrkit.MaldiSet property)
