Index

_

__init__() (mioXpektron.BatchDenoising method), [1] (mioXpektron.BatchTicNorm method), [1] (mioXpektron.denoise.BatchDenoising method), [1] (mioXpektron.denoise.DenoisingMethods method), [1] (mioXpektron.denoise.main.BatchDenoising method) (mioXpektron.denoise.main.DenoisingMethods method) (mioXpektron.DenoisingMethods method), [1] (mioXpektron.detection.detection.PeakAlignIntensityArea method) (mioXpektron.detection.PeakAlignIntensityArea method), [1] (mioXpektron.normalization.BatchTicNorm method), [1] (mioXpektron.normalization.preprocessing.BatchTicNorm method) (mioXpektron.PeakAlignIntensityArea method), [1] (mioXpektron.PlotPeaks method), [1] (mioXpektron.plotting.plot_peaks.PlotPeaks method) (mioXpektron.plotting.PlotPeaks method), [1]

A

agg_params (mioXpektron.baseline.flat_window_suggester.ScanForFlatRegion attribute) (mioXpektron.baseline.ScanForFlatRegion attribute), [1] (mioXpektron.ScanForFlatRegion attribute), [1] aggregate_common_windows() (in module mioXpektron.baseline.flat_window_suggester) aggregate_method_summaries() (in module mioXpektron.denoise.denoise_select) AggregateParams (class in mioXpektron), [1] (class in mioXpektron.baseline) (class in mioXpektron.baseline.flat_window_suggester) align_peaks() (in module mioXpektron), [1] (in module mioXpektron.detection), [1] (in module mioXpektron.detection.detection) alpha (mioXpektron.PlotPeaksConfig attribute), [1] (mioXpektron.plotting.plot_peaks.PlotPeaksConfig attribute) (mioXpektron.plotting.PlotPeaksConfig attribute), [1] apply() (mioXpektron.normalization.main.NormalizationMethods method) (mioXpektron.normalization.NormalizationMethods method), [1] (mioXpektron.NormalizationMethods method), [1] area (mioXpektron.denoise.denoise_select.PeakMeasurement attribute), [1] auto_scale_window_size (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator attribute) (mioXpektron.baseline.BaselineMethodEvaluator attribute), [1] (mioXpektron.BaselineMethodEvaluator attribute), [1] auto_screen_reference_masses (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] auto_tune (mioXpektron.baseline.flat_window_suggester.ScanForFlatRegion attribute) (mioXpektron.baseline.ScanForFlatRegion attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] (mioXpektron.ScanForFlatRegion attribute), [1] auto_tune_calib_config() (in module mioXpektron), [1] (in module mioXpektron.adaptive), [1] AutoCalibConfig (class in mioXpektron), [1] (class in mioXpektron.recalibrate), [1] (class in mioXpektron.recalibrate.auto_calibrator)

AutoCalibrator (class in mioXpektron), [1] (class in mioXpektron.recalibrate), [1] (class in mioXpektron.recalibrate.auto_calibrator) autodetect_fallback_policy (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] autodetect_method (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] autodetect_strategy (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] autodetect_tol_da (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] autodetect_tol_ppm (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] available_methods() (mioXpektron.normalization.main.NormalizationMethods static method) (mioXpektron.normalization.NormalizationMethods static method), [1] (mioXpektron.NormalizationMethods static method), [1]

B

baseline_correction() (in module mioXpektron), [1] (in module mioXpektron.baseline), [1] (in module mioXpektron.baseline.baseline_base) baseline_method (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2] baseline_method_names() (in module mioXpektron), [1] (in module mioXpektron.baseline) (in module mioXpektron.baseline.baseline_base) baseline_params (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2] BaselineBatchCorrector (class in mioXpektron), [1] (class in mioXpektron.baseline), [1] (class in mioXpektron.baseline.baseline_batch) BaselineMethodEvaluator (class in mioXpektron), [1] (class in mioXpektron.baseline), [1] (class in mioXpektron.baseline.baseline_eval) batch_denoise() (in module mioXpektron), [1] (in module mioXpektron.denoise) (in module mioXpektron.denoise.denoise_batch) batch_peak_process() (in module mioXpektron.recalibrate.peak_picker) batch_peak_process_uncal() (in module mioXpektron.recalibrate.peak_picker_uncal) batch_process_directory() (in module mioXpektron.recalibrate.auto_calibrator)

batch_processing() (in module mioXpektron.utils.main) batch_tic_norm() (in module mioXpektron), [1] (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.preprocessing) BatchDenoising (class in mioXpektron), [1] (class in mioXpektron.denoise), [1] (class in mioXpektron.denoise.main) BatchResult (class in mioXpektron.denoise.denoise_batch) BatchTicNorm (class in mioXpektron), [1] (class in mioXpektron.normalization), [1] (class in mioXpektron.normalization.preprocessing) bbi (mioXpektron.baseline.baseline_base.MetricResult attribute) best_method_map (mioXpektron.baseline.baseline_batch.BaselineBatchCorrector attribute) (mioXpektron.baseline.BaselineBatchCorrector attribute), [1] (mioXpektron.BaselineBatchCorrector attribute), [1] bh_fdr() (in module mioXpektron.utils.analysis) bin_width (mioXpektron.AggregateParams attribute), [1] (mioXpektron.baseline.AggregateParams attribute) (mioXpektron.baseline.flat_window_suggester.AggregateParams attribute) (mioXpektron.PlotPeaksConfig attribute), [1] (mioXpektron.plotting.plot_peaks.PlotPeaksConfig attribute) (mioXpektron.plotting.PlotPeaksConfig attribute), [1] br (mioXpektron.baseline.baseline_base.MetricResult attribute)

C

calibrate() (mioXpektron.AutoCalibrator method), [1] (mioXpektron.FlexibleCalibrator method), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibrator method) (mioXpektron.recalibrate.AutoCalibrator method), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibrator method) (mioXpektron.recalibrate.FlexibleCalibrator method), [1] calibrate_spectrum() (in module mioXpektron.recalibrate.calibrate_spectrum) calibration_method (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] CalibrationModel (class in mioXpektron.recalibrate.auto_calibrator) CENTROID (mioXpektron.recalibrate.auto_calibrator.PeakDetectionMethod attribute) CENTROID_RAW (mioXpektron.recalibrate.auto_calibrator.PeakDetectionMethod attribute) check_overlapping_peaks() (in module mioXpektron), [1] (in module mioXpektron.detection), [1] check_overlapping_peaks2() (in module mioXpektron), [1] (in module mioXpektron.detection), [1] choose_k_by_pac() (in module mioXpektron.utils.analysis) clip_negative (mioXpektron.baseline.baseline_batch.BaselineBatchCorrector attribute) (mioXpektron.baseline.BaselineBatchCorrector attribute), [1] (mioXpektron.BaselineBatchCorrector attribute), [1] clip_negative_after_baseline (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2] cluster_bootstrap_frac (mioXpektron.normalization.normalization_eval.NormalizationEvaluator attribute) (mioXpektron.normalization.NormalizationEvaluator attribute), [1] (mioXpektron.NormalizationEvaluator attribute), [1] cluster_bootstrap_rounds (mioXpektron.normalization.normalization_eval.NormalizationEvaluator attribute) (mioXpektron.normalization.NormalizationEvaluator attribute), [1] (mioXpektron.NormalizationEvaluator attribute), [1] collect_peak_properties_batch() (in module mioXpektron), [1] (in module mioXpektron.detection), [1] (in module mioXpektron.detection.detection) color_map (mioXpektron.PlotPeaksConfig attribute), [1] (mioXpektron.plotting.plot_peaks.PlotPeaksConfig attribute) (mioXpektron.plotting.PlotPeaksConfig attribute), [1]

compare() (mioXpektron.denoise.DenoisingMethods method), [1] (mioXpektron.denoise.main.DenoisingMethods method) (mioXpektron.DenoisingMethods method), [1] compare_across_files() (mioXpektron.denoise.DenoisingMethods class method), [1] (mioXpektron.denoise.main.DenoisingMethods class method) (mioXpektron.DenoisingMethods class method), [1] compare_denoising_methods() (in module mioXpektron), [1] (in module mioXpektron.denoise), [1] (in module mioXpektron.denoise.denoise_select) compare_in_windows() (mioXpektron.denoise.DenoisingMethods method), [1] (mioXpektron.denoise.main.DenoisingMethods method) (mioXpektron.DenoisingMethods method), [1] compare_methods_in_windows() (in module mioXpektron), [1] (in module mioXpektron.denoise) (in module mioXpektron.denoise.denoise_select) compare_visual() (mioXpektron.normalization.main.NormalizationMethods method) (mioXpektron.normalization.NormalizationMethods method), [1] (mioXpektron.NormalizationMethods method), [1] compute_metrics() (in module mioXpektron.baseline.baseline_base) compute_supervised (mioXpektron.normalization.normalization_eval.NormalizationEvaluator attribute) (mioXpektron.normalization.NormalizationEvaluator attribute), [1] (mioXpektron.NormalizationEvaluator attribute), [1] compute_univariate_tests() (in module mioXpektron.utils.analysis) corrected_intensities (mioXpektron.PlotPeak attribute), [1] (mioXpektron.plotting.plot.PlotPeak attribute) (mioXpektron.plotting.PlotPeak attribute), [1] coverage_threshold (mioXpektron.AggregateParams attribute), [1] (mioXpektron.baseline.AggregateParams attribute) (mioXpektron.baseline.flat_window_suggester.AggregateParams attribute) create_calibration_report() (in module mioXpektron.recalibrate.auto_calibrator) cumulative_figsize (mioXpektron.PlotPeaksConfig attribute), [1] (mioXpektron.plotting.plot_peaks.PlotPeaksConfig attribute) (mioXpektron.plotting.PlotPeaksConfig attribute), [1] curv_quantile (mioXpektron.baseline.flat_window_suggester.FlatParams attribute) (mioXpektron.baseline.FlatParams attribute) (mioXpektron.FlatParams attribute), [1]

D

data_dir (mioXpektron.PlotPeaksConfig attribute), [1] (mioXpektron.plotting.plot_peaks.PlotPeaksConfig attribute) (mioXpektron.plotting.PlotPeaksConfig attribute), [1] data_preprocessing() (in module mioXpektron), [1] (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.preprocessing) decode_method_label() (in module mioXpektron), [1] (in module mioXpektron.denoise) (in module mioXpektron.denoise.denoise_select) denoise_check() (mioXpektron.denoise.DenoisingMethods method), [1] (mioXpektron.denoise.main.DenoisingMethods method) (mioXpektron.DenoisingMethods method), [1] denoise_method (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2]

denoise_params (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2] DenoisingMethods (class in mioXpektron), [1] (class in mioXpektron.denoise), [1] (class in mioXpektron.denoise.main) detect_peaks_cwt_with_area() (in module mioXpektron), [1] (in module mioXpektron.detection), [1] (in module mioXpektron.detection.detection) detect_peaks_with_area() (in module mioXpektron), [1] (in module mioXpektron.detection), [1] (in module mioXpektron.detection.detection) detect_peaks_with_area_v2() (in module mioXpektron), [1] (in module mioXpektron.detection), [1] (in module mioXpektron.detection.detection) diagnose_calibration() (in module mioXpektron.recalibrate.auto_calibrator)

E

elapsed_s (mioXpektron.denoise.denoise_batch.BatchResult attribute) ensure_dir() (in module mioXpektron.utils.analysis) estimate_autodetect_tolerance() (in module mioXpektron), [1] (in module mioXpektron.adaptive), [1] estimate_bootstrap_heuristics() (in module mioXpektron), [1] (in module mioXpektron.adaptive), [1] estimate_denoise_params() (in module mioXpektron), [1] (in module mioXpektron.adaptive), [1] estimate_flat_params() (in module mioXpektron), [1] (in module mioXpektron.adaptive), [1] estimate_multisegment_breakpoints() (in module mioXpektron), [1] (in module mioXpektron.adaptive), [1] estimate_mz_tolerance() (in module mioXpektron), [1] (in module mioXpektron.adaptive), [1] estimate_normalization_target() (in module mioXpektron), [1] (in module mioXpektron.adaptive), [1] estimate_outlier_threshold() (in module mioXpektron), [1] (in module mioXpektron.adaptive), [1]

estimate_screening_thresholds() (in module mioXpektron), [1] (in module mioXpektron.adaptive), [1] eval_clip_negative (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator attribute) (mioXpektron.baseline.BaselineMethodEvaluator attribute), [1] (mioXpektron.BaselineMethodEvaluator attribute), [1] evaluate() (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator method) (mioXpektron.baseline.BaselineMethodEvaluator method), [1] (mioXpektron.BaselineMethodEvaluator method), [1] (mioXpektron.normalization.main.NormalizationMethods static method) (mioXpektron.normalization.normalization_eval.NormalizationEvaluator method) (mioXpektron.normalization.NormalizationEvaluator method), [1] (mioXpektron.normalization.NormalizationMethods static method), [1] (mioXpektron.NormalizationEvaluator method), [1] (mioXpektron.NormalizationMethods static method), [1] evaluate_one_method() (in module mioXpektron.normalization.normalization_eval) exclude_reference_masses (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1]

F

fail_on_high_error (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] figsize (mioXpektron.PlotPeaksConfig attribute), [1] (mioXpektron.plotting.plot_peaks.PlotPeaksConfig attribute) (mioXpektron.plotting.PlotPeaksConfig attribute), [1] file (mioXpektron.denoise.denoise_batch.BatchResult attribute) file_pattern (mioXpektron.PlotPeaksConfig attribute), [1] (mioXpektron.plotting.plot_peaks.PlotPeaksConfig attribute) (mioXpektron.plotting.PlotPeaksConfig attribute), [1] files (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator attribute) (mioXpektron.baseline.BaselineMethodEvaluator attribute), [1] (mioXpektron.baseline.flat_window_suggester.ScanForFlatRegion attribute) (mioXpektron.baseline.ScanForFlatRegion attribute), [1] (mioXpektron.BaselineMethodEvaluator attribute), [1] (mioXpektron.normalization.normalization_eval.NormalizationEvaluator attribute) (mioXpektron.normalization.NormalizationEvaluator attribute), [1] (mioXpektron.NormalizationEvaluator attribute), [1] (mioXpektron.PlotPeaks attribute) (mioXpektron.plotting.plot_peaks.PlotPeaks attribute) (mioXpektron.plotting.PlotPeaks attribute), [1] (mioXpektron.ScanForFlatRegion attribute), [1]

find_flat_segments() (in module mioXpektron.baseline.flat_window_suggester) flat_params (mioXpektron.baseline.flat_window_suggester.ScanForFlatRegion attribute) (mioXpektron.baseline.ScanForFlatRegion attribute), [1] (mioXpektron.ScanForFlatRegion attribute), [1] flat_windows (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator attribute) (mioXpektron.baseline.BaselineMethodEvaluator attribute), [1] (mioXpektron.BaselineMethodEvaluator attribute), [1] FlatParams (class in mioXpektron), [1] (class in mioXpektron.baseline) (class in mioXpektron.baseline.flat_window_suggester) FlexibleCalibConfig (class in mioXpektron), [1] (class in mioXpektron.recalibrate), [1] (class in mioXpektron.recalibrate.flexible_calibrator) FlexibleCalibConfigDebug (in module mioXpektron), [1] (in module mioXpektron.recalibrate) FlexibleCalibrator (class in mioXpektron), [1] (class in mioXpektron.recalibrate), [1] (class in mioXpektron.recalibrate.flexible_calibrator) FlexibleCalibratorDebug (class in mioXpektron), [1] (class in mioXpektron.recalibrate) (class in mioXpektron.recalibrate.flexible_calibrator_debug) fwhm_pts (mioXpektron.denoise.denoise_select.PeakMeasurement attribute), [1]

G

GAUSSIAN (mioXpektron.recalibrate.auto_calibrator.PeakDetectionMethod attribute) gaussian() (in module mioXpektron.detection.detection) get_group_counts() (mioXpektron.PlotPeaks method), [1] (mioXpektron.plotting.plot_peaks.PlotPeaks method) (mioXpektron.plotting.PlotPeaks method), [1] get_tic_statistics() (mioXpektron.BatchTicNorm method), [1] (mioXpektron.normalization.BatchTicNorm method), [1] (mioXpektron.normalization.preprocessing.BatchTicNorm method) grad_quantile (mioXpektron.baseline.flat_window_suggester.FlatParams attribute) (mioXpektron.baseline.FlatParams attribute) (mioXpektron.FlatParams attribute), [1]

group (mioXpektron.PlotPeak attribute), [1] (mioXpektron.plotting.plot.PlotPeak attribute) (mioXpektron.plotting.PlotPeak attribute), [1] group_fn (mioXpektron.normalization.normalization_eval.NormalizationEvaluator attribute) (mioXpektron.normalization.NormalizationEvaluator attribute), [1] (mioXpektron.NormalizationEvaluator attribute), [1] group_patterns (mioXpektron.normalization.normalization_eval.NormalizationEvaluator attribute) (mioXpektron.normalization.NormalizationEvaluator attribute), [1] (mioXpektron.NormalizationEvaluator attribute), [1] grouped_curves (mioXpektron.PlotPeaks attribute) (mioXpektron.plotting.plot_peaks.PlotPeaks attribute) (mioXpektron.plotting.PlotPeaks attribute), [1]

H

handle_missing_values() (in module mioXpektron.detection.detection)

height (mioXpektron.denoise.denoise_select.PeakMeasurement attribute), [1]

I

idx_center (mioXpektron.denoise.denoise_select.PeakMeasurement attribute), [1] import_data() (in module mioXpektron), [1] (in module mioXpektron.utils), [1] (in module mioXpektron.utils.file_management) in_dir (mioXpektron.baseline.baseline_batch.BaselineBatchCorrector attribute) (mioXpektron.baseline.BaselineBatchCorrector attribute), [1] (mioXpektron.BaselineBatchCorrector attribute), [1]

instrument_params (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1]

L

labels (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator attribute) (mioXpektron.baseline.BaselineMethodEvaluator attribute), [1] (mioXpektron.BaselineMethodEvaluator attribute), [1] last_autodetect_methods (mioXpektron.AutoCalibrator attribute) (mioXpektron.FlexibleCalibrator attribute) (mioXpektron.recalibrate.auto_calibrator.AutoCalibrator attribute) (mioXpektron.recalibrate.AutoCalibrator attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibrator attribute) (mioXpektron.recalibrate.FlexibleCalibrator attribute), [1] last_failed_or_excluded_files (mioXpektron.FlexibleCalibrator attribute) (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibrator attribute) (mioXpektron.recalibrate.FlexibleCalibrator attribute), [1] last_reference_mass_screening (mioXpektron.FlexibleCalibrator attribute) (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibrator attribute) (mioXpektron.recalibrate.FlexibleCalibrator attribute), [1] last_reference_masses_initial (mioXpektron.FlexibleCalibrator attribute) (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibrator attribute) (mioXpektron.recalibrate.FlexibleCalibrator attribute), [1]

last_reference_masses_screened_out (mioXpektron.FlexibleCalibrator attribute) (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibrator attribute) (mioXpektron.recalibrate.FlexibleCalibrator attribute), [1] last_reference_masses_used (mioXpektron.FlexibleCalibrator attribute) (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibrator attribute) (mioXpektron.recalibrate.FlexibleCalibrator attribute), [1] LINEAR_SQRT (mioXpektron.recalibrate.auto_calibrator.CalibrationModel attribute) load_and_measure_peaks_polars() (in module mioXpektron.detection.peak_analysis) load_data() (mioXpektron.PlotPeaks method), [1] (mioXpektron.plotting.plot_peaks.PlotPeaks method) (mioXpektron.plotting.PlotPeaks method), [1] load_txt_spectrum() (in module mioXpektron.denoise.denoise_batch) load_window() (mioXpektron.PlotPeaks static method), [1] (mioXpektron.plotting.plot_peaks.PlotPeaks static method) (mioXpektron.plotting.PlotPeaks static method), [1] local_centroid() (in module mioXpektron.recalibrate.calibrate_spectrum) log_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) lorentzian() (in module mioXpektron.detection.detection)

M

main() (in module mioXpektron.utils.analysis) mass_stratified_pqn_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) MAX (mioXpektron.recalibrate.auto_calibrator.PeakDetectionMethod attribute) max_iterations (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] max_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) max_ppm_error (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] max_ppm_threshold (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] max_ppm_warning (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] max_workers (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] median_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) median_of_ratios_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) message (mioXpektron.denoise.denoise_batch.BatchResult attribute) method (mioXpektron.baseline.baseline_batch.BaselineBatchCorrector attribute) (mioXpektron.baseline.BaselineBatchCorrector attribute), [1] (mioXpektron.BaselineBatchCorrector attribute), [1] method_kwargs (mioXpektron.baseline.baseline_batch.BaselineBatchCorrector attribute) (mioXpektron.baseline.BaselineBatchCorrector attribute), [1] (mioXpektron.BaselineBatchCorrector attribute), [1] method_kwargs_map (mioXpektron.normalization.normalization_eval.NormalizationEvaluator attribute) (mioXpektron.normalization.NormalizationEvaluator attribute), [1] (mioXpektron.NormalizationEvaluator attribute), [1] method_parameters() (mioXpektron.denoise.DenoisingMethods method), [1] (mioXpektron.denoise.main.DenoisingMethods method) (mioXpektron.DenoisingMethods method), [1] methods (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator attribute) (mioXpektron.baseline.BaselineMethodEvaluator attribute), [1] (mioXpektron.BaselineMethodEvaluator attribute), [1] (mioXpektron.normalization.normalization_eval.NormalizationEvaluator attribute) (mioXpektron.normalization.NormalizationEvaluator attribute), [1] (mioXpektron.NormalizationEvaluator attribute), [1] MetricResult (class in mioXpektron.baseline.baseline_base) metrics_for_composite (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator attribute) (mioXpektron.baseline.BaselineMethodEvaluator attribute), [1] (mioXpektron.BaselineMethodEvaluator attribute), [1] min_calibrants (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] min_points (mioXpektron.baseline.flat_window_suggester.FlatParams attribute) (mioXpektron.baseline.FlatParams attribute) (mioXpektron.FlatParams attribute), [1] min_width (mioXpektron.baseline.flat_window_suggester.FlatParams attribute) (mioXpektron.baseline.FlatParams attribute) (mioXpektron.FlatParams attribute), [1] minmax_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) mioXpektron module, [1] mioXpektron.adaptive module, [1] mioXpektron.baseline module mioXpektron.baseline.baseline_base module mioXpektron.baseline.baseline_batch module mioXpektron.baseline.baseline_eval module mioXpektron.baseline.baseline_main module mioXpektron.baseline.flat_window_suggester module mioXpektron.baseline.test_baseline_selection module mioXpektron.baseline.test_column_aliases module mioXpektron.denoise module mioXpektron.denoise.denoise_batch module mioXpektron.denoise.denoise_main module mioXpektron.denoise.denoise_select module mioXpektron.denoise.main module mioXpektron.denoise.test_denoise_selection module mioXpektron.detection module mioXpektron.detection.detection module mioXpektron.detection.peak_analysis module mioXpektron.detection.test_noise_models module mioXpektron.normalization module mioXpektron.normalization.main module mioXpektron.normalization.normalization module mioXpektron.normalization.normalization_eval module mioXpektron.normalization.preprocessing module

mioXpektron.normalization.tic_count module mioXpektron.pipeline module mioXpektron.plotting module mioXpektron.plotting.plot module mioXpektron.plotting.plot_peaks module mioXpektron.recalibrate module mioXpektron.recalibrate.auto_calibrator module mioXpektron.recalibrate.calibrate_spectrum module mioXpektron.recalibrate.flexible_calibrator module mioXpektron.recalibrate.flexible_calibrator_debug module mioXpektron.recalibrate.peak_picker module mioXpektron.recalibrate.peak_picker_uncal module mioXpektron.recalibrate.test_diagnostic module mioXpektron.utils module mioXpektron.utils.analysis module mioXpektron.utils.file_management module mioXpektron.utils.main module model (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] models_to_try (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] module mioXpektron, [1] mioXpektron.adaptive, [1] mioXpektron.baseline mioXpektron.baseline.baseline_base mioXpektron.baseline.baseline_batch mioXpektron.baseline.baseline_eval mioXpektron.baseline.baseline_main mioXpektron.baseline.flat_window_suggester mioXpektron.baseline.test_baseline_selection mioXpektron.baseline.test_column_aliases mioXpektron.denoise mioXpektron.denoise.denoise_batch mioXpektron.denoise.denoise_main mioXpektron.denoise.denoise_select mioXpektron.denoise.main mioXpektron.denoise.test_denoise_selection mioXpektron.detection mioXpektron.detection.detection mioXpektron.detection.peak_analysis mioXpektron.detection.test_noise_models mioXpektron.normalization mioXpektron.normalization.main mioXpektron.normalization.normalization mioXpektron.normalization.normalization_eval mioXpektron.normalization.preprocessing mioXpektron.normalization.tic_count mioXpektron.pipeline mioXpektron.plotting mioXpektron.plotting.plot mioXpektron.plotting.plot_peaks mioXpektron.recalibrate mioXpektron.recalibrate.auto_calibrator mioXpektron.recalibrate.calibrate_spectrum mioXpektron.recalibrate.flexible_calibrator mioXpektron.recalibrate.flexible_calibrator_debug mioXpektron.recalibrate.peak_picker mioXpektron.recalibrate.peak_picker_uncal mioXpektron.recalibrate.test_diagnostic mioXpektron.utils mioXpektron.utils.analysis mioXpektron.utils.file_management mioXpektron.utils.main multi_ion_reference_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) MULTISEGMENT (mioXpektron.recalibrate.auto_calibrator.CalibrationModel attribute) multisegment_breakpoints (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] mz_center (mioXpektron.denoise.denoise_select.PeakMeasurement attribute), [1] mz_left (mioXpektron.denoise.denoise_select.PeakMeasurement attribute) mz_max (mioXpektron.normalization.normalization_eval.NormalizationEvaluator attribute) (mioXpektron.normalization.NormalizationEvaluator attribute), [1] (mioXpektron.NormalizationEvaluator attribute), [1] (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2] (mioXpektron.PlotPeaksConfig attribute), [1] (mioXpektron.plotting.plot_peaks.PlotPeaksConfig attribute) (mioXpektron.plotting.PlotPeaksConfig attribute), [1] mz_min (mioXpektron.normalization.normalization_eval.NormalizationEvaluator attribute) (mioXpektron.normalization.NormalizationEvaluator attribute), [1] (mioXpektron.NormalizationEvaluator attribute), [1] (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2] (mioXpektron.PlotPeaksConfig attribute), [1] (mioXpektron.plotting.plot_peaks.PlotPeaksConfig attribute) (mioXpektron.plotting.PlotPeaksConfig attribute), [1] mz_right (mioXpektron.denoise.denoise_select.PeakMeasurement attribute) mz_rounding_precision (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2] mz_tolerance (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2] mz_values (mioXpektron.PlotPeak attribute), [1] (mioXpektron.plotting.plot.PlotPeak attribute) (mioXpektron.plotting.PlotPeak attribute), [1]

N

n_clusters (mioXpektron.normalization.normalization_eval.NormalizationEvaluator attribute) (mioXpektron.normalization.NormalizationEvaluator attribute), [1] (mioXpektron.NormalizationEvaluator attribute), [1] n_jobs (mioXpektron.baseline.baseline_batch.BaselineBatchCorrector attribute) (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator attribute) (mioXpektron.baseline.BaselineBatchCorrector attribute), [1] (mioXpektron.baseline.BaselineMethodEvaluator attribute), [1] (mioXpektron.baseline.flat_window_suggester.ScanForFlatRegion attribute) (mioXpektron.baseline.ScanForFlatRegion attribute), [1] (mioXpektron.BaselineBatchCorrector attribute), [1] (mioXpektron.BaselineMethodEvaluator attribute), [1] (mioXpektron.normalization.normalization_eval.NormalizationEvaluator attribute) (mioXpektron.normalization.NormalizationEvaluator attribute), [1] (mioXpektron.NormalizationEvaluator attribute), [1] (mioXpektron.ScanForFlatRegion attribute), [1] n_points (mioXpektron.denoise.denoise_batch.BatchResult attribute) nar (mioXpektron.baseline.baseline_base.MetricResult attribute) nbc (mioXpektron.baseline.baseline_base.MetricResult attribute) noise_filtering() (in module mioXpektron), [1] (in module mioXpektron.denoise), [1] (in module mioXpektron.denoise.denoise_main) norm_tic (mioXpektron.PlotPeaksConfig attribute), [1] (mioXpektron.plotting.plot_peaks.PlotPeaksConfig attribute) (mioXpektron.plotting.PlotPeaksConfig attribute), [1]

normalization_method_names() (in module mioXpektron), [1] (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) normalization_target (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2] normalization_target() (in module mioXpektron), [1] (in module mioXpektron.normalization) (in module mioXpektron.normalization.tic_count) NormalizationEvaluator (class in mioXpektron), [1] (class in mioXpektron.normalization), [1] (class in mioXpektron.normalization.normalization_eval) NormalizationMethods (class in mioXpektron), [1] (class in mioXpektron.normalization), [1] (class in mioXpektron.normalization.main) normalize() (in module mioXpektron), [1] (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) normalize_and_check() (mioXpektron.normalization.main.NormalizationMethods method) (mioXpektron.normalization.NormalizationMethods method), [1] (mioXpektron.NormalizationMethods method), [1]

O

out_dir (mioXpektron.baseline.flat_window_suggester.ScanForFlatRegion attribute) (mioXpektron.baseline.ScanForFlatRegion attribute), [1] (mioXpektron.ScanForFlatRegion attribute), [1] out_file (mioXpektron.denoise.denoise_batch.BatchResult attribute) outlier_threshold (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1]

output_folder (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] output_folder_calibrated (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2] output_mz_range (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1]

P

PARABOLIC (mioXpektron.recalibrate.auto_calibrator.PeakDetectionMethod attribute) param_grid (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator attribute) (mioXpektron.baseline.BaselineMethodEvaluator attribute), [1] (mioXpektron.BaselineMethodEvaluator attribute), [1] pareto_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) pattern (mioXpektron.baseline.baseline_batch.BaselineBatchCorrector attribute) (mioXpektron.baseline.BaselineBatchCorrector attribute), [1] (mioXpektron.BaselineBatchCorrector attribute), [1] PeakAlignIntensityArea (class in mioXpektron), [1] (class in mioXpektron.detection), [1] (class in mioXpektron.detection.detection) PeakDetectionMethod (class in mioXpektron.recalibrate.auto_calibrator) PeakMeasurement (class in mioXpektron.denoise.denoise_select) per_file_best (mioXpektron.baseline.baseline_batch.BaselineBatchCorrector attribute) (mioXpektron.baseline.BaselineBatchCorrector attribute), [1] (mioXpektron.BaselineBatchCorrector attribute), [1] PHYSICAL (mioXpektron.recalibrate.auto_calibrator.CalibrationModel attribute) pick_peaks() (in module mioXpektron.recalibrate.peak_picker) (in module mioXpektron.recalibrate.peak_picker_uncal) PipelineConfig (class in mioXpektron), [1], [2] (class in mioXpektron.pipeline) plot() (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator method) (mioXpektron.baseline.BaselineMethodEvaluator method), [1] (mioXpektron.BaselineMethodEvaluator method), [1] (mioXpektron.denoise.DenoisingMethods method), [1] (mioXpektron.denoise.main.DenoisingMethods method) (mioXpektron.DenoisingMethods method), [1] (mioXpektron.normalization.normalization_eval.NormalizationEvaluator method) (mioXpektron.normalization.NormalizationEvaluator method), [1] (mioXpektron.NormalizationEvaluator method), [1] (mioXpektron.PlotPeak method), [1] (mioXpektron.plotting.plot.PlotPeak method) (mioXpektron.plotting.PlotPeak method), [1] plot_all() (mioXpektron.PlotPeaks method), [1] (mioXpektron.plotting.plot_peaks.PlotPeaks method) (mioXpektron.plotting.PlotPeaks method), [1] plot_cumulative() (mioXpektron.PlotPeaks method), [1] (mioXpektron.plotting.plot_peaks.PlotPeaks method) (mioXpektron.plotting.PlotPeaks method), [1] plot_heatmap_top_features() (in module mioXpektron.utils.analysis) plot_overlapping_peaks() (in module mioXpektron), [1] (in module mioXpektron.plotting) (in module mioXpektron.plotting.plot_peaks)

plot_overlay() (mioXpektron.PlotPeaks method), [1] (mioXpektron.plotting.plot_peaks.PlotPeaks method) (mioXpektron.plotting.PlotPeaks method), [1] plot_pareto_delta_snr_vs_height() (in module mioXpektron), [1] (in module mioXpektron.denoise) (in module mioXpektron.denoise.denoise_select) plot_pca() (in module mioXpektron.utils.analysis) plot_umap() (in module mioXpektron.utils.analysis) plot_volcano() (in module mioXpektron.utils.analysis) PlotPeak (class in mioXpektron), [1] (class in mioXpektron.plotting), [1] (class in mioXpektron.plotting.plot) PlotPeaks (class in mioXpektron), [1] (class in mioXpektron.plotting), [1] (class in mioXpektron.plotting.plot_peaks) PlotPeaksConfig (class in mioXpektron), [1] (class in mioXpektron.plotting), [1] (class in mioXpektron.plotting.plot_peaks) poisson_scaling() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) POLY2 (mioXpektron.recalibrate.auto_calibrator.CalibrationModel attribute) pqn_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) prefer_physical_models (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] prefer_recompute_from_channel (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] preview_overlay() (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator method) (mioXpektron.baseline.BaselineMethodEvaluator method), [1] (mioXpektron.BaselineMethodEvaluator method), [1] (mioXpektron.normalization.normalization_eval.NormalizationEvaluator method) (mioXpektron.normalization.NormalizationEvaluator method), [1] (mioXpektron.NormalizationEvaluator method), [1] print_summary() (mioXpektron.normalization.normalization_eval.NormalizationEvaluator method) (mioXpektron.normalization.NormalizationEvaluator method), [1] (mioXpektron.NormalizationEvaluator method), [1] process() (mioXpektron.BatchTicNorm method), [1] (mioXpektron.normalization.BatchTicNorm method), [1] (mioXpektron.normalization.preprocessing.BatchTicNorm method) prominence (mioXpektron.denoise.denoise_select.PeakMeasurement attribute), [1]

Q

QUAD_SQRT (mioXpektron.recalibrate.auto_calibrator.CalibrationModel attribute)

quick_calibrate() (in module mioXpektron.recalibrate.auto_calibrator)

R

random_state (mioXpektron.normalization.normalization_eval.NormalizationEvaluator attribute) (mioXpektron.normalization.NormalizationEvaluator attribute), [1] (mioXpektron.NormalizationEvaluator attribute), [1] rank_method() (in module mioXpektron), [1] (in module mioXpektron.denoise), [1] (in module mioXpektron.denoise.denoise_select) rank_methods_pandas() (in module mioXpektron.denoise.denoise_select) rank_methods_polars() (in module mioXpektron.denoise.denoise_select) raw_intensities (mioXpektron.PlotPeak attribute), [1] (mioXpektron.plotting.plot.PlotPeak attribute) (mioXpektron.plotting.PlotPeak attribute), [1] raw_noise_quantile (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator attribute) (mioXpektron.baseline.BaselineMethodEvaluator attribute), [1] (mioXpektron.BaselineMethodEvaluator attribute), [1] read_spectrum_table() (in module mioXpektron.baseline.baseline_base) (in module mioXpektron.baseline.flat_window_suggester) recursive (mioXpektron.baseline.baseline_batch.BaselineBatchCorrector attribute) (mioXpektron.baseline.BaselineBatchCorrector attribute), [1] (mioXpektron.BaselineBatchCorrector attribute), [1] reference_masses (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] REFLECTRON (mioXpektron.recalibrate.auto_calibrator.CalibrationModel attribute) resample_spectrum() (in module mioXpektron), [1] (in module mioXpektron.normalization) (in module mioXpektron.normalization.preprocessing) retry_high_error_max_removals (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] retry_high_error_with_mz_fallback (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1]

retry_high_error_with_pruning (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] rfzn (mioXpektron.baseline.baseline_base.MetricResult attribute) rms_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) robust_noise_estimation() (in module mioXpektron), [1] (in module mioXpektron.detection), [1] (in module mioXpektron.detection.detection) robust_noise_estimation_mz() (in module mioXpektron), [1] (in module mioXpektron.detection) (in module mioXpektron.detection.detection) robust_noise_estimation_mz_dependent() (in module mioXpektron.detection), [1] (in module mioXpektron.detection.detection) robust_peak_detection() (in module mioXpektron), [1] (in module mioXpektron.detection), [1] (in module mioXpektron.detection.detection) robust_snv_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) run() (mioXpektron.baseline.baseline_batch.BaselineBatchCorrector method) (mioXpektron.baseline.BaselineBatchCorrector method), [1] (mioXpektron.baseline.flat_window_suggester.ScanForFlatRegion method) (mioXpektron.baseline.ScanForFlatRegion method), [1] (mioXpektron.BaselineBatchCorrector method), [1] (mioXpektron.BatchDenoising method), [1] (mioXpektron.denoise.BatchDenoising method), [1] (mioXpektron.denoise.main.BatchDenoising method) (mioXpektron.detection.detection.PeakAlignIntensityArea method) (mioXpektron.detection.PeakAlignIntensityArea method), [1] (mioXpektron.PeakAlignIntensityArea method), [1] (mioXpektron.ScanForFlatRegion method), [1] run_cnmf() (in module mioXpektron.utils.analysis) run_models() (in module mioXpektron.utils.analysis) run_pipeline() (in module mioXpektron), [1] (in module mioXpektron.pipeline)

S

sample_name (mioXpektron.PlotPeak attribute), [1] (mioXpektron.plotting.plot.PlotPeak attribute) (mioXpektron.plotting.PlotPeak attribute), [1] save_consensus_heatmap() (in module mioXpektron.utils.analysis) save_diagnostic_plots (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] save_factor_bars() (in module mioXpektron.utils.analysis) save_fig (mioXpektron.PlotPeaksConfig attribute), [1] (mioXpektron.plotting.plot_peaks.PlotPeaksConfig attribute) (mioXpektron.plotting.PlotPeaksConfig attribute), [1] save_path (mioXpektron.PlotPeaksConfig attribute), [1] (mioXpektron.plotting.plot_peaks.PlotPeaksConfig attribute) (mioXpektron.plotting.PlotPeaksConfig attribute), [1] save_plots (mioXpektron.baseline.baseline_batch.BaselineBatchCorrector attribute) (mioXpektron.baseline.BaselineBatchCorrector attribute), [1] (mioXpektron.BaselineBatchCorrector attribute), [1] save_txt_spectrum() (in module mioXpektron.denoise.denoise_batch) savgol_poly (mioXpektron.baseline.flat_window_suggester.FlatParams attribute) (mioXpektron.baseline.FlatParams attribute) (mioXpektron.FlatParams attribute), [1] savgol_window (mioXpektron.baseline.flat_window_suggester.FlatParams attribute) (mioXpektron.baseline.FlatParams attribute) (mioXpektron.FlatParams attribute), [1] ScanForFlatRegion (class in mioXpektron), [1] (class in mioXpektron.baseline), [1] (class in mioXpektron.baseline.flat_window_suggester) screen_exclude_below_mz (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] screen_max_mean_abs_ppm (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] screen_max_median_abs_ppm (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] screen_min_count (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1]

screen_min_valid_fraction (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] select_methods() (in module mioXpektron), [1] (in module mioXpektron.denoise), [1] (in module mioXpektron.denoise.denoise_select) select_stable_reference_masses() (in module mioXpektron.recalibrate.flexible_calibrator) selected_ion_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) set_group_inference() (mioXpektron.PlotPeaks method), [1] (mioXpektron.plotting.plot_peaks.PlotPeaks method) (mioXpektron.plotting.PlotPeaks method), [1] show_group_cumulative (mioXpektron.PlotPeaksConfig attribute), [1] (mioXpektron.plotting.plot_peaks.PlotPeaksConfig attribute) (mioXpektron.plotting.PlotPeaksConfig attribute), [1] show_median (mioXpektron.PlotPeaksConfig attribute), [1] (mioXpektron.plotting.plot_peaks.PlotPeaksConfig attribute) (mioXpektron.plotting.PlotPeaksConfig attribute), [1] small_param_grid_preset() (in module mioXpektron), [1] (in module mioXpektron.baseline) (in module mioXpektron.baseline.baseline_base) snr (mioXpektron.baseline.baseline_base.MetricResult attribute) snv_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) specs (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator attribute) (mioXpektron.baseline.BaselineMethodEvaluator attribute), [1] (mioXpektron.BaselineMethodEvaluator attribute), [1] spectral_angle() (in module mioXpektron.normalization.normalization_eval) SPLINE (mioXpektron.recalibrate.auto_calibrator.CalibrationModel attribute) spline_smoothing (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1] sqrt_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) status (mioXpektron.denoise.denoise_batch.BatchResult attribute) summarize_reference_mass_stability() (in module mioXpektron.recalibrate.flexible_calibrator)

T

test_aggregate_method_summaries_preserves_unique_methods() (in module mioXpektron.denoise.test_denoise_selection) test_baseline_correction_accepts_parameterized_method_labels() (in module mioXpektron.baseline.test_baseline_selection) test_build_denoising_method_grid_excludes_derivatives_by_default() (in module mioXpektron.denoise.test_denoise_selection) test_column_aliases() (in module mioXpektron.baseline.test_column_aliases) test_compare_across_files_aggregates_sample_level_summaries() (in module mioXpektron.denoise.test_denoise_selection) test_compare_in_windows_ranks_aggregated_rollup() (in module mioXpektron.denoise.test_denoise_selection) test_detect_peaks_with_area_supports_mz_binned_thresholds() (in module mioXpektron.detection.test_noise_models) test_detect_peaks_with_area_v2_supports_mz_binned_thresholds() (in module mioXpektron.detection.test_noise_models) test_detect_peaks_with_area_v2_uses_shared_height_threshold_helper() (in module mioXpektron.detection.test_noise_models) test_evaluator_uses_param_grid_keys_when_methods_are_omitted() (in module mioXpektron.baseline.test_baseline_selection) test_measure_on_method_rejects_monotonic_shoulder() (in module mioXpektron.denoise.test_denoise_selection) test_peak_align_intensity_area_forwards_deconvolution_controls() (in module mioXpektron.detection.test_noise_models) test_peak_align_intensity_area_forwards_noise_model() (in module mioXpektron.detection.test_noise_models) test_plot_pareto_falls_back_to_all_finite_candidates_when_none_pass() (in module mioXpektron.denoise.test_denoise_selection) test_preview_overlay_uses_ranked_parameterized_methods() (in module mioXpektron.baseline.test_baseline_selection)

test_rank_methods_pandas_applies_ppm_normalized_selection_criteria() (in module mioXpektron.denoise.test_denoise_selection) test_robust_noise_estimation_excludes_full_peak_width_not_only_center_window() (in module mioXpektron.detection.test_noise_models) test_robust_noise_estimation_mz_dependent_tracks_local_noise_levels() (in module mioXpektron.detection.test_noise_models) test_select_methods_constrained_pareto_then_snr_prefers_highest_snr() (in module mioXpektron.denoise.test_denoise_selection) tic_normalization() (in module mioXpektron), [1] (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) to_ppm() (in module mioXpektron.denoise.denoise_select) top_k (mioXpektron.AggregateParams attribute), [1] (mioXpektron.baseline.AggregateParams attribute) (mioXpektron.baseline.flat_window_suggester.AggregateParams attribute) topk_for_snr (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator attribute) (mioXpektron.baseline.BaselineMethodEvaluator attribute), [1] (mioXpektron.BaselineMethodEvaluator attribute), [1] two_gaussians() (in module mioXpektron.detection.detection)

U

use_bootstrap_init (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] use_outlier_rejection (mioXpektron.AutoCalibConfig attribute), [1] (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.auto_calibrator.AutoCalibConfig attribute) (mioXpektron.recalibrate.AutoCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1]

use_recalibration (mioXpektron.pipeline.PipelineConfig attribute) (mioXpektron.PipelineConfig attribute), [1], [2] use_small_param_preset (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator attribute) (mioXpektron.baseline.BaselineMethodEvaluator attribute), [1] (mioXpektron.BaselineMethodEvaluator attribute), [1]

V

validate_calibration() (in module mioXpektron.recalibrate.auto_calibrator) vector_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization) verbose (mioXpektron.FlexibleCalibConfig attribute), [1] (mioXpektron.recalibrate.flexible_calibrator.FlexibleCalibConfig attribute) (mioXpektron.recalibrate.FlexibleCalibConfig attribute), [1]

VOIGT (mioXpektron.recalibrate.auto_calibrator.PeakDetectionMethod attribute) voigt() (in module mioXpektron.detection.detection) vsn_normalization() (in module mioXpektron.normalization), [1] (in module mioXpektron.normalization.normalization)

W

warning_log() (mioXpektron.baseline.baseline_eval.BaselineMethodEvaluator method) (mioXpektron.baseline.BaselineMethodEvaluator method), [1] (mioXpektron.BaselineMethodEvaluator method), [1]

wavelet_denoise() (in module mioXpektron.denoise.denoise_main) within_group_mean_sam() (in module mioXpektron.normalization.normalization_eval)

Y

y_quantile (mioXpektron.baseline.flat_window_suggester.FlatParams attribute) (mioXpektron.baseline.FlatParams attribute) (mioXpektron.FlatParams attribute), [1]

Z

zoom() (mioXpektron.PlotPeak method), [1] (mioXpektron.plotting.plot.PlotPeak method) (mioXpektron.plotting.PlotPeak method), [1]