Modules¶
- calibration
- fdr
get_q_values()keep_best()BinaryClassifierLegacyNewBatchingClassifierFeedForwardNNFeedForwardNN.T_destinationFeedForwardNN.__init__()FeedForwardNN.add_module()FeedForwardNN.apply()FeedForwardNN.bfloat16()FeedForwardNN.buffers()FeedForwardNN.call_super_initFeedForwardNN.children()FeedForwardNN.compile()FeedForwardNN.cpu()FeedForwardNN.cuda()FeedForwardNN.double()FeedForwardNN.dump_patchesFeedForwardNN.eval()FeedForwardNN.extra_repr()FeedForwardNN.float()FeedForwardNN.forward()FeedForwardNN.get_buffer()FeedForwardNN.get_extra_state()FeedForwardNN.get_parameter()FeedForwardNN.get_submodule()FeedForwardNN.half()FeedForwardNN.ipu()FeedForwardNN.load_state_dict()FeedForwardNN.modules()FeedForwardNN.mtia()FeedForwardNN.named_buffers()FeedForwardNN.named_children()FeedForwardNN.named_modules()FeedForwardNN.named_parameters()FeedForwardNN.parameters()FeedForwardNN.register_backward_hook()FeedForwardNN.register_buffer()FeedForwardNN.register_forward_hook()FeedForwardNN.register_forward_pre_hook()FeedForwardNN.register_full_backward_hook()FeedForwardNN.register_full_backward_pre_hook()FeedForwardNN.register_load_state_dict_post_hook()FeedForwardNN.register_load_state_dict_pre_hook()FeedForwardNN.register_module()FeedForwardNN.register_parameter()FeedForwardNN.register_state_dict_post_hook()FeedForwardNN.register_state_dict_pre_hook()FeedForwardNN.requires_grad_()FeedForwardNN.set_extra_state()FeedForwardNN.set_submodule()FeedForwardNN.share_memory()FeedForwardNN.state_dict()FeedForwardNN.to()FeedForwardNN.to_empty()FeedForwardNN.train()FeedForwardNN.trainingFeedForwardNN.type()FeedForwardNN.xpu()FeedForwardNN.zero_grad()
plot_fdr()manage_torch_threads()train_test_split_()
- _fdrx
- fragcomp
- libtransform
- outputtransform
build_run_internal_df()build_run_stat_df()log_stat_df()transfer_library_stat_df()- Output Accumulator
AccumulationBroadcasterBaseAccumulatorTransferLearningAccumulatorbuild_speclibflat_from_quant()error_callback()ms2_quality_control()normalize_rt_delta_max()normalize_rt_max()perform_protein_fdr()SearchPlanOutputSearchPlanOutput.INTERNAL_OUTPUTSearchPlanOutput.LIBRARY_OUTPUTSearchPlanOutput.PG_OUTPUTSearchPlanOutput.PRECURSOR_OUTPUTSearchPlanOutput.PSM_INPUTSearchPlanOutput.STAT_OUTPUTSearchPlanOutput.TRANSFER_MODELSearchPlanOutput.TRANSFER_OUTPUTSearchPlanOutput.TRANSFER_STATS_OUTPUTSearchPlanOutput.__init__()SearchPlanOutput.build()
apply_output_column_names()apply_protein_inference()get_channels_from_config()load_psm_files_from_folders()log_protein_fdr_summary()merge_quant_levels_to_psm()prepare_psm_dataframe()read_df()write_df()
- search_step
- search.selection
CandidateSelectionCandidateContainerCandidateSelectionConfigCandidateSelectionConfigJITCandidateSelectionConfigJIT.candidate_countCandidateSelectionConfigJIT.center_fractionCandidateSelectionConfigJIT.class_typeCandidateSelectionConfigJIT.exclude_shared_ionsCandidateSelectionConfigJIT.f_mobilityCandidateSelectionConfigJIT.f_rtCandidateSelectionConfigJIT.feature_meanCandidateSelectionConfigJIT.feature_stdCandidateSelectionConfigJIT.feature_weightCandidateSelectionConfigJIT.fragment_mz_toleranceCandidateSelectionConfigJIT.group_channelsCandidateSelectionConfigJIT.isotope_toleranceCandidateSelectionConfigJIT.join_close_candidatesCandidateSelectionConfigJIT.join_close_candidates_cycle_thresholdCandidateSelectionConfigJIT.join_close_candidates_scan_thresholdCandidateSelectionConfigJIT.kernel_sizeCandidateSelectionConfigJIT.max_size_mobilityCandidateSelectionConfigJIT.max_size_rtCandidateSelectionConfigJIT.min_size_mobilityCandidateSelectionConfigJIT.min_size_rtCandidateSelectionConfigJIT.mobility_toleranceCandidateSelectionConfigJIT.peak_len_mobilityCandidateSelectionConfigJIT.peak_len_rtCandidateSelectionConfigJIT.precursor_mz_toleranceCandidateSelectionConfigJIT.rt_toleranceCandidateSelectionConfigJIT.sigma_scale_mobilityCandidateSelectionConfigJIT.sigma_scale_rtCandidateSelectionConfigJIT.top_k_fragmentsCandidateSelectionConfigJIT.top_k_precursorsCandidateSelectionConfigJIT.use_weighted_score
PrecursorFlatContainerPrecursorFlatContainer.candidate_start_idxPrecursorFlatContainer.candidate_stop_idxPrecursorFlatContainer.chargePrecursorFlatContainer.class_typePrecursorFlatContainer.frag_start_idxPrecursorFlatContainer.frag_stop_idxPrecursorFlatContainer.isotopesPrecursorFlatContainer.mobilityPrecursorFlatContainer.mzPrecursorFlatContainer.precursor_idxPrecursorFlatContainer.rt
candidate_container_to_df()NumbaContextOnlyconvolve_fourier()GaussianKernelmultivariate_normal()amean1()assemble_isotope_mz()astd1()find_peaks_1d()find_peaks_2d()slice_manual()symetric_limits_2d()wrap0()wrap1()
- search.scoring
CandidateScoringCandidateScoring.__init__()CandidateScoring.assemble_fragments()CandidateScoring.assemble_score_group_container()CandidateScoring.collect_candidates()CandidateScoring.collect_fragments()CandidateScoring.configCandidateScoring.dia_dataCandidateScoring.fragments_flat_dfCandidateScoring.merge_candidate_data()CandidateScoring.merge_precursor_data()CandidateScoring.precursors_flat_dfCandidateScoring.quadrupole_calibration
CandidateScoringConfigCandidateScoringConfig.__init__()CandidateScoringConfig.collect_fragmentsCandidateScoringConfig.exclude_shared_ionsCandidateScoringConfig.experimental_xicCandidateScoringConfig.fragment_mz_toleranceCandidateScoringConfig.precursor_mz_toleranceCandidateScoringConfig.quant_allCandidateScoringConfig.quant_windowCandidateScoringConfig.reference_channelCandidateScoringConfig.score_groupedCandidateScoringConfig.top_k_fragmentsCandidateScoringConfig.top_k_isotopesCandidateScoringConfig.validate()
CandidateScoringConfigJITOutputPsmDFcorrelation_coefficient()median_axis()normalize_profiles()calculate_score_groups()candidate_features_to_candidates()fragment_correlation()fragment_correlation_different()frame_profile_1d()frame_profile_2d()merge_missing_columns()multiplex_candidates()or_envelope_1d()or_envelope_2d()save_corrcoeff()scan_profile_1d()scan_profile_2d()slice()tile()SimpleQuadrupoleSimpleQuadrupoleJitcalculate_observation_importance_single()calculate_template_single()expand_cycle()logistic()logistic_rectangle()quadrupole_transfer_function_single()- Features
- utils
- validation
- workflow
WorkflowBaseWorkflowBase.CALIBRATION_MANAGER_PKL_NAMEWorkflowBase.FDR_MANAGER_PKL_NAMEWorkflowBase.OPTIMIZATION_MANAGER_PKL_NAMEWorkflowBase.RAW_FILE_MANAGER_PKL_NAMEWorkflowBase.TIMING_MANAGER_PKL_NAMEWorkflowBase.__init__()WorkflowBase.calibration_managerWorkflowBase.configWorkflowBase.dia_dataWorkflowBase.load()WorkflowBase.optimization_managerWorkflowBase.pathWorkflowBase.spectral_libraryWorkflowBase.timing_manager
Config
- workflow.managers
BaseManagerCalibrationEstimatorsCalibrationGroupsCalibrationManagerFDRManagercolumn_hash()get_group_columns()OptimizationManagerOptimizationManager.__init__()OptimizationManager.classifier_versionOptimizationManager.fwhm_mobilityOptimizationManager.fwhm_rtOptimizationManager.mobility_errorOptimizationManager.ms1_errorOptimizationManager.ms2_errorOptimizationManager.num_candidatesOptimizationManager.rt_errorOptimizationManager.score_cutoffOptimizationManager.update()
RawFileManagerTimingManager