Index

A

a (tidyms2.chem.Isotope attribute) abundance (tidyms2.simulation.base.BaseChemicalSpeciesSpec attribute) (tidyms2.simulation.lcms.SimulatedLCMSAdductSpec attribute) accumulate_spectra() (in module tidyms2.algorithms.raw) accumulator (tidyms2.algorithms.raw.MakeChromatogramParameters attribute) add_columns() (tidyms2.core.matrix.DataMatrix method) add_feature_groups() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) add_features() (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemorySampleStorage method) add_fill_values() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) add_rois() (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemorySampleStorage method) add_sample_data() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method)

adduct_annotated (tidyms2.core.dataflow.AssayProcessStatus attribute) (tidyms2.core.dataflow.SampleProcessStatus attribute) adducts (tidyms2.simulation.lcms.SimulatedLCMSSampleFactory attribute) aggregated descriptor annotation (tidyms2.core.models.AnnotableFeature attribute) (tidyms2.core.models.Feature attribute) (tidyms2.core.models.FeatureGroup attribute) apex (tidyms2.lcms.Peak attribute) apply() (tidyms2.core.operators.matrix.MatrixOperator method) (tidyms2.core.operators.sample.SampleOperator method) area (tidyms2.core.models.AnnotableFeature property) (tidyms2.core.models.Feature property) (tidyms2.lcms.Peak property) assay ASSAY (tidyms2.core.enums.OperatorType attribute) AssayStorage (class in tidyms2.core.storage)

B

base_response_factor (tidyms2.simulation.base.InstrumentResponseSpec attribute) base_snr (tidyms2.simulation.base.MeasurementNoiseSpec attribute) baseline (tidyms2.core.models.MZTrace attribute) batch (tidyms2.core.models.SampleMetadata attribute)

bounds (tidyms2.chem.EnvelopeScorerConfiguration attribute) (tidyms2.chem.EnvelopeValidatorConfiguration attribute) (tidyms2.chem.FormulaGeneratorConfiguration attribute) (tidyms2.core.operators.sample.FeatureExtractor attribute)

C

centroid (tidyms2.core.models.MSSpectrum attribute) charge (tidyms2.core.models.Annotation attribute) (tidyms2.core.models.GroupAnnotation attribute) check_process_status() (in module tidyms2.core.dataflow) check_status() (tidyms2.core.matrix.DataMatrix method) (tidyms2.core.operators.base.BaseOperator method) ChemicalContext (class in tidyms2.chem) combine() (tidyms2.core.matrix.DataMatrix class method) compare() (tidyms2.core.models.AnnotableFeature method) (tidyms2.lcms.Peak method) compute_abundance() (tidyms2.simulation.base.BaseChemicalSpeciesSpec method) (tidyms2.simulation.lcms.SimulatedLCMSAdductSpec method) compute_fill_values() (tidyms2.core.operators.assay.MissingImputer method) compute_intensity() (tidyms2.simulation.base.BaseChemicalSpeciesSpec method) (tidyms2.simulation.lcms.SimulatedLCMSAdductSpec method) compute_isotopic_envelope() (tidyms2.core.models.AnnotableFeature static method) (tidyms2.lcms.Peak static method) compute_patches() (tidyms2.core.operators.assay.AnnotationPatcher method) (tidyms2.core.operators.assay.DescriptorPatcher method) (tidyms2.lcms.LCFeatureMatcher method)

compute_response_factor() (tidyms2.simulation.base.InstrumentResponseSpec method) compute_sample_rt() (tidyms2.simulation.lcms.RtSpec method) compute_snr() (tidyms2.simulation.base.MeasurementNoiseSpec method) config (tidyms2.simulation.lcms.SimulatedLCMSSample attribute) consensus annotation context (tidyms2.chem.EnvelopeScorerConfiguration attribute) (tidyms2.chem.EnvelopeValidatorConfiguration attribute) correlation() (tidyms2.core.matrix.DataMatrix.Metrics method) create() (tidyms2.simulation.base.MZGridSpec method) create_features() (tidyms2.simulation.lcms.SimulatedLCMSSampleFactory method) create_lcms_assay() (in module tidyms2.lcms) create_simulated_features() (tidyms2.simulation.lcms.SimulatedLCMSAdductSpec method) create_simulated_sample_spec() (tidyms2.simulation.lcms.SimulatedLCMSSampleFactory method) create_snapshot() (tidyms2.core.storage.AssayStorage method) (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.OnMemorySampleStorage method) (tidyms2.storage.SQLiteAssayStorage method) create_submatrix() (tidyms2.core.matrix.DataMatrix method) cv() (tidyms2.core.matrix.DataMatrix.Metrics method)

D

d (tidyms2.chem.Isotope property) data matrix data_acquisition (tidyms2.simulation.lcms.SimulatedLCMSSampleFactory attribute) DataMatrix (class in tidyms2.core.matrix) DataMatrix.IO (class in tidyms2.core.matrix) DataMatrix.Metrics (class in tidyms2.core.matrix) DataMatrix.Query (class in tidyms2.core.matrix) DBSCAN delete_features() (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemorySampleStorage method)

delete_rois() (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemorySampleStorage method) describe() (tidyms2.core.models.AnnotableFeature method) (tidyms2.core.models.Feature method) descriptor (tidyms2.core.models.DescriptorPatch attribute) descriptor_names() (tidyms2.core.models.AnnotableFeature class method) (tidyms2.core.models.Feature class method) descriptors (tidyms2.core.models.FeatureGroup attribute) detect_peaks() (in module tidyms2.algorithms.signal) detection_rate() (tidyms2.core.matrix.DataMatrix.Metrics method) dratio() (tidyms2.core.matrix.DataMatrix.Metrics method)

E

EIC end (tidyms2.lcms.Peak attribute) end_time (tidyms2.algorithms.raw.AccumulateSpectraParameters attribute) (tidyms2.core.models.Sample attribute) envelope (tidyms2.core.models.GroupAnnotation attribute) EnvelopeScorer (class in tidyms2.chem) EnvelopeValidator (class in tidyms2.chem) equals() (tidyms2.core.models.MZTrace method) estimate_baseline() (in module tidyms2.algorithms.signal) estimate_noise() (in module tidyms2.algorithms.signal)

exclude (tidyms2.core.operators.matrix.ColumnFilter attribute) (tidyms2.core.operators.matrix.ColumnTransformer attribute) (tidyms2.core.operators.matrix.RowFilter attribute) (tidyms2.core.operators.matrix.RowTransformer attribute) extension (tidyms2.lcms.Peak property) extra (tidyms2.core.dataflow.AssayProcessStatus attribute) (tidyms2.core.dataflow.BaseProcessStatus attribute) (tidyms2.core.dataflow.DataMatrixProcessStatus attribute) (tidyms2.core.dataflow.SampleProcessStatus attribute) extract_features() (tidyms2.lcms.LCPeakExtractor method) extract_rois() (tidyms2.lcms.LCTraceExtractor method)

F

feature (tidyms2.core.matrix.FeatureVector attribute) feature descriptor feature group feature matching feature_extracted (tidyms2.core.dataflow.SampleProcessStatus attribute) feature_group (tidyms2.core.models.FillValue attribute) feature_matched (tidyms2.core.dataflow.AssayProcessStatus attribute) features (tidyms2.core.matrix.DataMatrix property) (tidyms2.simulation.lcms.SimulatedLCMSSample attribute) features_group_created (tidyms2.core.dataflow.AssayProcessStatus attribute) features_to_csv() (tidyms2.core.matrix.DataMatrix.IO method) features_to_dict() (tidyms2.core.matrix.DataMatrix.IO method) fetch_annotations() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) fetch_descriptors() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) fetch_feature_groups() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) fetch_features_by_group() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) fetch_features_by_id() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) fetch_features_by_sample() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) fetch_fill_values() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) fetch_rois_by_id() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method)

fetch_rois_by_sample() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) fetch_sample() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) fetch_sample_data() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) fetch_sample_ids() (tidyms2.core.matrix.DataMatrix.Query method) field (tidyms2.core.models.AnnotationPatch attribute) fill_missing (tidyms2.algorithms.raw.MakeChromatogramParameters attribute) filter() (tidyms2.chem.EnvelopeScorer method) (tidyms2.chem.EnvelopeValidator method) (tidyms2.core.matrix.DataMatrix.Query method) find_centroids() (in module tidyms2.algorithms.signal) Formula (class in tidyms2.chem) formula (tidyms2.simulation.base.BaseChemicalSpeciesSpec attribute) (tidyms2.simulation.lcms.SimulatedLCMSAdductSpec attribute) FormulaGenerator (class in tidyms2.chem) from_chnops() (tidyms2.chem.EnvelopeScorerConfiguration class method) (tidyms2.chem.EnvelopeValidatorConfiguration class method) (tidyms2.chem.FormulaGeneratorConfiguration class method) from_csv() (tidyms2.core.matrix.DataMatrix.IO class method) from_defaults() (tidyms2.core.operators.base.BaseOperator class method) (tidyms2.lcms.LCFeatureMatcher class method) (tidyms2.lcms.LCPeakExtractor class method) (tidyms2.lcms.LCTraceBaselineEstimator class method) (tidyms2.lcms.LCTraceExtractor class method) (tidyms2.lcms.LCTraceSmoother class method) from_dict() (tidyms2.storage.OnMemorySampleStorage class method) from_sample_storage() (tidyms2.storage.OnMemorySampleStorage class method) from_str() (tidyms2.core.models.AnnotableFeature class method) (tidyms2.core.models.Feature class method) (tidyms2.core.models.MZTrace class method) (tidyms2.core.models.Roi class method)

G

generate_envelopes() (tidyms2.chem.EnvelopeScorer method) (tidyms2.chem.EnvelopeValidator method) generate_formulas() (tidyms2.chem.FormulaGenerator method) get() (tidyms2.core.models.AnnotableFeature method) (tidyms2.core.models.Feature method) get_chromatogram() (tidyms2.MSData method) (tidyms2.simulation.lcms.SimulatedLCMSDataReader method) get_columns() (tidyms2.core.matrix.DataMatrix method) get_data() (tidyms2.core.matrix.DataMatrix method) get_element() (tidyms2.chem.PeriodicTable method) get_exact_mass() (tidyms2.chem.Formula method) get_expected_status_in() (tidyms2.core.operators.assay.AnnotationPatcher method) (tidyms2.core.operators.assay.DescriptorPatcher method) (tidyms2.core.operators.assay.MissingImputer method) (tidyms2.core.operators.base.BaseOperator method) (tidyms2.core.operators.sample.FeatureExtractor method) (tidyms2.core.operators.sample.FeatureTransformer method) (tidyms2.core.operators.sample.RoiExtractor method) (tidyms2.core.operators.sample.RoiTransformer method) get_expected_status_out() (tidyms2.core.operators.assay.AnnotationPatcher method) (tidyms2.core.operators.assay.DescriptorPatcher method) (tidyms2.core.operators.assay.MissingImputer method) (tidyms2.core.operators.base.BaseOperator method) (tidyms2.core.operators.sample.FeatureExtractor method) (tidyms2.core.operators.sample.FeatureTransformer method) (tidyms2.core.operators.sample.RoiExtractor method) (tidyms2.core.operators.sample.RoiTransformer method) get_extra() (tidyms2.core.dataflow.AssayProcessStatus method) (tidyms2.core.dataflow.BaseProcessStatus method) (tidyms2.core.dataflow.DataMatrixProcessStatus method) (tidyms2.core.dataflow.SampleProcessStatus method) get_feature() (tidyms2.core.matrix.DataMatrix method) (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemorySampleStorage method) get_feature_index() (tidyms2.core.matrix.DataMatrix method) get_feature_type() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) get_isotope() (tidyms2.chem.PeriodicTable method) get_isotopic_envelope() (tidyms2.chem.Formula method) get_mz() (tidyms2.simulation.base.BaseChemicalSpeciesSpec method) (tidyms2.simulation.lcms.SimulatedLCMSAdductSpec method) get_n_chromatograms() (tidyms2.MSData method) (tidyms2.simulation.lcms.SimulatedLCMSDataReader method) get_n_features() (tidyms2.core.matrix.DataMatrix method) (tidyms2.core.storage.AssayStorage method) (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.OnMemorySampleStorage method) (tidyms2.storage.SQLiteAssayStorage method)

get_n_results() (tidyms2.chem.FormulaGenerator method) get_n_rois() (tidyms2.core.storage.AssayStorage method) (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.OnMemorySampleStorage method) (tidyms2.storage.SQLiteAssayStorage method) get_n_samples() (tidyms2.core.matrix.DataMatrix method) (tidyms2.storage.SQLiteAssayStorage method) get_n_spectra() (tidyms2.MSData method) (tidyms2.simulation.lcms.SimulatedLCMSDataReader method) get_nbytes() (tidyms2.core.models.MSSpectrum method) get_nominal_mass() (tidyms2.chem.Formula method) get_process_status() (tidyms2.core.matrix.DataMatrix method) (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) get_results() (tidyms2.chem.FormulaGenerator method) get_roi() (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemorySampleStorage method) get_roi_type() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) get_rows() (tidyms2.core.matrix.DataMatrix method) get_sample() (tidyms2.core.matrix.DataMatrix method) (tidyms2.core.storage.SampleStorage method) (tidyms2.MSData method) (tidyms2.storage.OnMemorySampleStorage method) get_sample_index() (tidyms2.core.matrix.DataMatrix method) get_sensitivity_loss_factor() (tidyms2.simulation.base.InstrumentResponseSpec method) get_slice_height() (tidyms2.core.models.MZTrace method) get_snapshot_id() (tidyms2.core.storage.AssayStorage method) (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.OnMemorySampleStorage method) (tidyms2.storage.SQLiteAssayStorage method) get_spectrum() (tidyms2.MSData method) (tidyms2.simulation.lcms.SimulatedLCMSDataReader method) get_status() (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemorySampleStorage method) get_top_results() (tidyms2.chem.EnvelopeScorer method) grid (tidyms2.simulation.base.DataAcquisitionSpec attribute) group (tidyms2.core.models.Annotation attribute) (tidyms2.core.models.FeatureGroup attribute) (tidyms2.core.models.SampleMetadata attribute) group_by() (tidyms2.core.matrix.DataMatrix.Query method)

H

has_descriptors_in_range() (tidyms2.core.models.AnnotableFeature method) (tidyms2.core.models.Feature method) (tidyms2.core.models.FeatureGroup method) has_feature() (tidyms2.core.matrix.DataMatrix method) (tidyms2.core.storage.AssayStorage method) (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.OnMemorySampleStorage method) (tidyms2.storage.SQLiteAssayStorage method) has_feature_group() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method)

has_roi() (tidyms2.core.storage.AssayStorage method) (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.OnMemorySampleStorage method) (tidyms2.storage.SQLiteAssayStorage method) has_sample() (tidyms2.core.matrix.DataMatrix method) (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) height (tidyms2.core.models.AnnotableFeature property) (tidyms2.core.models.Feature property) (tidyms2.lcms.Peak property) high (tidyms2.simulation.base.MZGridSpec attribute)

I

id (tidyms2.core.models.AnnotableFeature attribute) (tidyms2.core.models.Annotation attribute) (tidyms2.core.models.AnnotationPatch attribute) (tidyms2.core.models.Chromatogram attribute) (tidyms2.core.models.DescriptorPatch attribute) (tidyms2.core.models.Feature attribute) (tidyms2.core.models.MSSpectrum attribute) (tidyms2.core.models.MZTrace attribute) (tidyms2.core.models.Roi attribute) (tidyms2.core.models.Sample attribute) (tidyms2.core.models.TidyMSBaseModel attribute) (tidyms2.core.operators.base.BaseOperator attribute) index (tidyms2.core.models.Chromatogram attribute)

int (tidyms2.core.models.Chromatogram attribute) (tidyms2.core.models.MSSpectrum attribute) (tidyms2.simulation.lcms.SimulatedLCMSFeature attribute) int_std (tidyms2.simulation.base.DataAcquisitionSpec attribute) interbatch_variation (tidyms2.simulation.base.InstrumentResponseSpec attribute) io (tidyms2.core.matrix.DataMatrix property) is_monoisotope() (tidyms2.chem.PeriodicTable method) isotopes (tidyms2.chem.Element attribute) isotopologue_annotated (tidyms2.core.dataflow.AssayProcessStatus attribute) (tidyms2.core.dataflow.SampleProcessStatus attribute) isotopologue_group (tidyms2.core.models.GroupAnnotation attribute) isotopologue_index (tidyms2.core.models.Annotation attribute) (tidyms2.core.models.GroupAnnotation attribute) isotopologue_label (tidyms2.core.models.Annotation attribute)

K

kind (tidyms2.algorithms.raw.MakeTICParameters attribute)

L

label (tidyms2.core.models.GroupAnnotation attribute) LC-MS list_extras() (tidyms2.core.dataflow.AssayProcessStatus method) (tidyms2.core.dataflow.BaseProcessStatus method) (tidyms2.core.dataflow.DataMatrixProcessStatus method) (tidyms2.core.dataflow.SampleProcessStatus method) list_feature_groups() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) list_features() (tidyms2.core.matrix.DataMatrix method) (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemorySampleStorage method) list_rois() (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemorySampleStorage method)

list_sample_field() (tidyms2.core.matrix.DataMatrix method) list_samples() (tidyms2.core.matrix.DataMatrix method) (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) list_snapshots() (tidyms2.core.storage.AssayStorage method) (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.OnMemorySampleStorage method) (tidyms2.storage.SQLiteAssayStorage method) lod() (tidyms2.core.matrix.DataMatrix.Metrics method) loq() (tidyms2.core.matrix.DataMatrix.Metrics method) low (tidyms2.simulation.base.MZGridSpec attribute)

M

m (tidyms2.chem.Isotope attribute) m/z make_chromatograms() (in module tidyms2.algorithms.raw) make_grid() (tidyms2.simulation.lcms.SimulatedLCMSSample method) make_roi() (in module tidyms2.algorithms.raw) make_tic() (in module tidyms2.algorithms.raw) MATRIX (tidyms2.core.enums.OperatorType attribute) matrix_to_csv() (tidyms2.core.matrix.DataMatrix.IO method) matrix_to_dict() (tidyms2.core.matrix.DataMatrix.IO method) max_length (tidyms2.chem.EnvelopeScorerConfiguration attribute) (tidyms2.chem.EnvelopeValidatorConfiguration attribute) max_M (tidyms2.chem.EnvelopeScorerConfiguration attribute) (tidyms2.chem.EnvelopeValidatorConfiguration attribute) (tidyms2.chem.FormulaGeneratorConfiguration attribute) max_M_tol (tidyms2.chem.EnvelopeValidatorConfiguration attribute) max_missing (tidyms2.algorithms.raw.MakeRoiParameters attribute) max_sensitivity_loss (tidyms2.simulation.base.InstrumentResponseSpec attribute) mean (tidyms2.simulation.base.AbundanceSpec attribute) (tidyms2.simulation.lcms.RtSpec attribute) meta (tidyms2.core.models.Sample attribute) metrics (tidyms2.core.matrix.DataMatrix property) min_int (tidyms2.simulation.base.DataAcquisitionSpec attribute) min_intensity (tidyms2.algorithms.raw.MakeRoiParameters attribute) min_length (tidyms2.algorithms.raw.MakeRoiParameters attribute) min_M_tol (tidyms2.chem.EnvelopeValidatorConfiguration attribute) min_proba (tidyms2.lcms.LCTraceBaselineEstimator attribute) min_slice_size (tidyms2.lcms.LCTraceBaselineEstimator attribute) min_snr (tidyms2.simulation.base.MeasurementNoiseSpec attribute) missing_imputed (tidyms2.core.dataflow.AssayProcessStatus attribute) (tidyms2.core.dataflow.DataMatrixProcessStatus attribute) mmi (tidyms2.chem.Element property) module tidyms2.algorithms.raw tidyms2.algorithms.signal tidyms2.chem tidyms2.core.dataflow tidyms2.core.matrix tidyms2.core.models tidyms2.core.operators.assay tidyms2.core.operators.base tidyms2.core.operators.matrix tidyms2.core.operators.sample tidyms2.core.storage tidyms2.io.matrix tidyms2.lcms tidyms2.simulation.base tidyms2.simulation.lcms tidyms2.storage

monoisotope (tidyms2.chem.Element property) ms_data_mode (tidyms2.core.models.Sample attribute) ms_level (tidyms2.algorithms.raw.AccumulateSpectraParameters attribute) (tidyms2.core.models.MSSpectrum attribute) (tidyms2.core.models.Sample attribute) (tidyms2.simulation.base.DataAcquisitionSpec attribute) MSData (class in tidyms2) MSInstrument (class in tidyms2.core.enums) multiple_match (tidyms2.algorithms.raw.MakeRoiParameters attribute) mz (tidyms2.algorithms.raw.MakeChromatogramParameters attribute) (tidyms2.core.models.AnnotableFeature property) (tidyms2.core.models.Feature property) (tidyms2.core.models.FeatureGroup property) (tidyms2.core.models.IsotopicEnvelope attribute) (tidyms2.core.models.MSSpectrum attribute) (tidyms2.core.models.MZTrace attribute) (tidyms2.lcms.Peak property) (tidyms2.simulation.lcms.SimulatedLCMSFeature attribute) mz_std (tidyms2.lcms.Peak property) (tidyms2.simulation.base.DataAcquisitionSpec attribute) mz_tolerance (tidyms2.lcms.LCFeatureMatcher attribute) mz_width (tidyms2.simulation.base.DataAcquisitionSpec attribute)

N

n (tidyms2.chem.Isotope property) n_isotopologues (tidyms2.simulation.base.BaseChemicalSpeciesSpec attribute) (tidyms2.simulation.lcms.SimulatedLCMSAdductSpec attribute) n_scans (tidyms2.simulation.base.DataAcquisitionSpec attribute) n_slices (tidyms2.lcms.LCTraceBaselineEstimator attribute) name (tidyms2.chem.Element attribute) (tidyms2.core.models.Chromatogram attribute) (tidyms2.core.models.GroupAnnotation attribute)

noise (tidyms2.core.models.MZTrace attribute) (tidyms2.simulation.base.BaseChemicalSpeciesSpec attribute) (tidyms2.simulation.lcms.SimulatedLCMSAdductSpec attribute) normalized (tidyms2.core.dataflow.DataMatrixProcessStatus attribute)

O

OnMemoryAssayStorage (class in tidyms2.storage) OnMemorySampleStorage (class in tidyms2.storage)

OperatorType (class in tidyms2.core.enums) order (tidyms2.core.models.SampleMetadata attribute)

P

p (tidyms2.chem.Isotope attribute) (tidyms2.core.models.IsotopicEnvelope attribute) p_tol (tidyms2.chem.EnvelopeValidatorConfiguration attribute) pad (tidyms2.algorithms.raw.MakeRoiParameters attribute) patch_annotations() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method)

patch_descriptors() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method) path (tidyms2.core.models.Sample attribute) pca() (tidyms2.core.matrix.DataMatrix.Metrics method) PeriodicTable (class in tidyms2.chem) prevalence (tidyms2.simulation.base.AbundanceSpec attribute) ProgenesisReaderError

Q

query (tidyms2.core.matrix.DataMatrix property)

R

read_progenesis() (in module tidyms2.io.matrix) reader (tidyms2.core.models.Sample attribute) remove_elements_with_a_single_isotope() (tidyms2.chem.EnvelopeValidatorConfiguration method) remove_features() (tidyms2.core.matrix.DataMatrix method) remove_samples() (tidyms2.core.matrix.DataMatrix method) response (tidyms2.simulation.base.BaseChemicalSpeciesSpec attribute) (tidyms2.simulation.lcms.SimulatedLCMSAdductSpec attribute) results_to_array() (tidyms2.chem.FormulaGenerator method) robust (tidyms2.lcms.LCTraceBaselineEstimator attribute) ROI

roi (tidyms2.core.models.AnnotableFeature attribute) (tidyms2.core.models.Feature attribute) roi_extracted (tidyms2.core.dataflow.SampleProcessStatus attribute) roi_id (tidyms2.core.models.Annotation attribute) Rt rt (tidyms2.lcms.Peak property) (tidyms2.simulation.lcms.SimulatedLCMSAdductSpec attribute) (tidyms2.simulation.lcms.SimulatedLCMSFeature attribute) rt_end (tidyms2.lcms.Peak property) rt_start (tidyms2.lcms.Peak property) rt_tolerance (tidyms2.lcms.LCFeatureMatcher attribute)

S

sample SAMPLE (tidyms2.core.enums.OperatorType attribute) sample (tidyms2.core.matrix.SampleVector attribute) (tidyms2.core.models.MZTrace attribute) (tidyms2.core.models.Roi attribute) sample group sample type sample_abundance() (tidyms2.simulation.base.AbundanceSpec method) sample_id (tidyms2.core.models.Annotation attribute) (tidyms2.core.models.FillValue attribute) sample_noise() (tidyms2.simulation.base.MeasurementNoiseSpec method) samples (tidyms2.core.matrix.DataMatrix property) samples_to_csv() (tidyms2.core.matrix.DataMatrix.IO method) samples_to_dict() (tidyms2.core.matrix.DataMatrix.IO method) SampleStorage (class in tidyms2.core.storage) scan (tidyms2.core.models.MZTrace attribute) score() (tidyms2.chem.EnvelopeScorer method) score_envelope() (in module tidyms2.chem) sensitivity_decay (tidyms2.simulation.base.InstrumentResponseSpec attribute) serialize_path() (tidyms2.core.models.Sample method) set_columns() (tidyms2.core.matrix.DataMatrix method) set_data() (tidyms2.core.matrix.DataMatrix method) set_extra() (tidyms2.core.dataflow.AssayProcessStatus method) (tidyms2.core.dataflow.BaseProcessStatus method) (tidyms2.core.dataflow.DataMatrixProcessStatus method) (tidyms2.core.dataflow.SampleProcessStatus method) set_process_status() (tidyms2.core.storage.AssayStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.SQLiteAssayStorage method)

set_rows() (tidyms2.core.matrix.DataMatrix method) set_snapshot() (tidyms2.core.storage.AssayStorage method) (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemoryAssayStorage method) (tidyms2.storage.OnMemorySampleStorage method) (tidyms2.storage.SQLiteAssayStorage method) set_status() (tidyms2.core.storage.SampleStorage method) (tidyms2.storage.OnMemorySampleStorage method) simulate_data_matrix() (in module tidyms2.simulation.lcms) SimulatedLCMSDataReader (class in tidyms2.simulation.lcms) size (tidyms2.simulation.base.MZGridSpec attribute) smooth() (in module tidyms2.algorithms.signal) smoothing_strength (tidyms2.lcms.LCTraceBaselineEstimator attribute) SNR snr (tidyms2.lcms.Peak property) spint (tidyms2.core.models.MZTrace attribute) sql() (tidyms2.core.matrix.DataMatrix.Query method) SQLiteAssayStorage (class in tidyms2.storage) start (tidyms2.lcms.Peak attribute) start_time (tidyms2.algorithms.raw.AccumulateSpectraParameters attribute) (tidyms2.core.models.Sample attribute) status (tidyms2.core.matrix.DataMatrix property) std (tidyms2.simulation.base.AbundanceSpec attribute) (tidyms2.simulation.lcms.RtSpec attribute) strength (tidyms2.lcms.LCTraceSmoother attribute) subtract_left_time (tidyms2.algorithms.raw.AccumulateSpectraParameters attribute) subtract_right_time (tidyms2.algorithms.raw.AccumulateSpectraParameters attribute) symbol (tidyms2.chem.Element attribute) (tidyms2.chem.Isotope attribute)

T

targeted_mz (tidyms2.algorithms.raw.MakeRoiParameters attribute) tidyms2.algorithms.raw module tidyms2.algorithms.signal module tidyms2.chem module tidyms2.core.dataflow module tidyms2.core.matrix module tidyms2.core.models module tidyms2.core.operators.assay module tidyms2.core.operators.base module tidyms2.core.operators.matrix module tidyms2.core.operators.sample module tidyms2.core.storage module

tidyms2.io.matrix module tidyms2.lcms module tidyms2.simulation.base module tidyms2.simulation.lcms module tidyms2.storage module time (tidyms2.core.models.Chromatogram attribute) (tidyms2.core.models.MSSpectrum attribute) (tidyms2.core.models.MZTrace attribute) time_resolution (tidyms2.simulation.base.DataAcquisitionSpec attribute) to_str() (tidyms2.chem.Isotope method) (tidyms2.core.models.AnnotableFeature method) (tidyms2.core.models.Feature method) (tidyms2.core.models.MZTrace method) (tidyms2.core.models.Roi method) tolerance (tidyms2.algorithms.raw.MakeRoiParameters attribute) transform_roi() (tidyms2.lcms.LCTraceBaselineEstimator method) (tidyms2.lcms.LCTraceSmoother method) type (tidyms2.core.models.SampleMetadata attribute)

U

update_bounds() (tidyms2.chem.EnvelopeScorerConfiguration method) (tidyms2.chem.EnvelopeValidatorConfiguration method) (tidyms2.chem.FormulaGeneratorConfiguration method)

update_process_status() (in module tidyms2.core.dataflow) update_status() (tidyms2.core.operators.base.BaseOperator method) using_tmp_config() (tidyms2.MSData method)

V

validate() (tidyms2.core.matrix.DataMatrix method) value (tidyms2.core.models.AnnotationPatch attribute) (tidyms2.core.models.DescriptorPatch attribute) (tidyms2.core.models.FillValue attribute)

W

width (tidyms2.lcms.Peak property) (tidyms2.simulation.lcms.RtSpec attribute) (tidyms2.simulation.lcms.SimulatedLCMSFeature attribute)

window (tidyms2.algorithms.raw.MakeChromatogramParameters attribute)

Z

z (tidyms2.chem.Element attribute) (tidyms2.chem.Isotope attribute)