Index

A

aa_match() (proteobench.score.denovoscores.DenovoScores method) aa_match_prefix() (proteobench.score.denovoscores.DenovoScores method) add() (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationReport method) add_current_data_point() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.quant.quant_base_module.QuantModule method) add_error() (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationReport method) add_features() (proteobench.io.parsing.parse_settings.ParseSettingsDeNovo method) add_fixed_mod() (in module proteobench.io.parsing.utils) add_info() (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationReport method) add_keywords_column_to_submitted_data() (in module webinterface.pages.base_pages.tabs.tab2_upload_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab2_upload_results) add_maxquant_fixed_modifications() (in module proteobench.io.parsing.utils) add_modification_parser() (proteobench.io.parsing.parse_settings.ParseSettingsDeNovo method) (proteobench.io.parsing.parse_settings.ParseSettingsEntrapment method) (proteobench.io.parsing.parse_settings.ParseSettingsQuant method) add_open_source_column() (in module webinterface.pages.base_pages.utils.resulttable) add_record() (in module proteobench.io.params.maxquant) add_warning() (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationReport method) additional_params_json (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) aggregate_modification_column() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) aggregate_modification_sites_column() (in module proteobench.io.parsing.parse_ion) all_datapoints (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) all_datapoints_submission (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute)

all_datapoints_submitted (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) allowed_miscleavages (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] alpha_warning (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) apply_parameter_filters() (in module webinterface.pages.base_pages.utils.parameter_filters) archived_warning (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) available_profiles() (in module proteobench.validation) (in module proteobench.validation.profiles)

B

BaseStreamlitUI (class in webinterface.pages.base) BaseUIModule (class in webinterface.pages.base_pages.base) benchmarking() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.denovo.denovo_DDA_HCD.DDAHCDDeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.entrapment.entrapment_ion_DIA_Astral.DIAEntrapmentIonModuleAstral method) (proteobench.modules.quant.quant_base_module.QuantModule method) (proteobench.modules.quant.quant_lfq_ion_DDA_Astral.DDAQuantIonAstralModule method) (proteobench.modules.quant.quant_lfq_ion_DDA_QExactive.DDAQuantIonModuleQExactive method) (proteobench.modules.quant.quant_lfq_ion_DIA_AIF.DIAQuantIonModuleAIF method) (proteobench.modules.quant.quant_lfq_ion_DIA_Astral.DIAQuantIonModuleAstral method) (proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF.DIAQuantIonModulediaPASEF method) (proteobench.modules.quant.quant_lfq_ion_DIA_Plasma.DIAQuantIonModulePlasma method) (proteobench.modules.quant.quant_lfq_ion_DIA_singlecell.DIAQuantIonModulediaSC method) (proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF.DIAQuantIonModuleZenoTOF method) (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule method) (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule method) benchmarking_2() (proteobench.modules.quant.quant_lfq_ion_DDA_Astral.DDAQuantIonAstralModule method) beta_warning (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute)

build_parser() (proteobench.io.parsing.parse_settings.ParseSettingsBuilder method) build_Series_from_records() (in module proteobench.io.params.maxquant) build_submissions_figure() (in module webinterface.UI_utils) build_tool_pie_chart() (in module webinterface.UI_utils) button_submission_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute)

C

calculate_fdp_at_fdr_thresholds() (proteobench.score.entrapmentscores.EntrapmentScores static method) calculate_lower_bound_fdp() (proteobench.score.entrapmentscores.EntrapmentScores static method) calculate_metrics() (proteobench.score.entrapmentscores.EntrapmentScores static method) calculate_paired_fdp() (proteobench.score.entrapmentscores.EntrapmentScores static method) calculate_prc() (in module proteobench.datapoint.denovo_datapoint) calculate_reported_fdr() (proteobench.score.entrapmentscores.EntrapmentScores static method) calculate_upper_bound_combined_fdp() (proteobench.score.entrapmentscores.EntrapmentScores static method) categorise_metric() (proteobench.score.entrapmentscores.EntrapmentScores static method) category (webinterface.pages.utils.module_registry.ModuleMetadata attribute) category_combined (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute) category_paired (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute) charge_column (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] Check (class in proteobench.validation) (class in proteobench.validation.profiles) check (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] check_charge_range() (in module proteobench.validation.checks) check_enzyme() (in module proteobench.validation.checks) check_fdr_psm() (in module proteobench.validation.checks) check_mass_tolerances() (in module proteobench.validation.checks) check_max_modifications() (in module proteobench.validation.checks) check_modifications() (in module proteobench.validation.checks) check_names (proteobench.validation.profiles.ValidationProfile property) (proteobench.validation.ValidationProfile property) check_new_unique_hash() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.quant.quant_base_module.QuantModule method) check_peptide_length() (in module proteobench.validation.checks) check_protein_ids() (in module proteobench.validation.checks) check_run_consistency() (in module proteobench.validation.checks) check_submission (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) check_submission_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) CheckFunc (in module proteobench.validation.profiles) checkpoint (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) checks (proteobench.validation.profiles.ValidationProfile attribute), [1] (proteobench.validation.ValidationProfile attribute), [1] clean_dataframe_for_export() (in module webinterface.pages.base_pages.utils.general) clean_line() (in module proteobench.io.params.alphadia) clean_text() (in module proteobench.io.params.peaks) (in module proteobench.io.params.spectronaut) clean_up_parameters() (in module proteobench.io.params.alphadia) clear_highlight_column() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) clone() (proteobench.github.gh.GithubProteobotRepo static method) clone_pr() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.quant.quant_base_module.QuantModule method) clone_repo() (proteobench.github.gh.GithubProteobotRepo method) clone_repo_anonymous() (proteobench.github.gh.GithubProteobotRepo method) clone_repo_pr() (proteobench.github.gh.GithubProteobotRepo method) code (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] collapse_aa_scores() (in module proteobench.datapoint.denovo_datapoint) colorblind_mode_selector_indepth_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute)

colorblind_mode_selector_submitted_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) colorblind_mode_selector_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) combined_FDP (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] comment (proteobench.io.params.fragger.Parameter attribute) comments (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] comments_submission_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) commit() (proteobench.github.gh.GithubProteobotRepo method) compare_dictionaries() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) compute_condition_stats() (proteobench.score.QuantScoresHYE static method) (proteobench.score.quantscoresHYE.QuantScoresHYE static method) compute_epsilon() (proteobench.score.QuantScoresHYE static method) (proteobench.score.quantscoresHYE.QuantScoresHYE static method) compute_roc_auc() (in module proteobench.datapoint.quant_datapoint) compute_roc_auc_directional() (in module proteobench.datapoint.quant_datapoint) config (proteobench.validation.context.ValidationContext attribute), [1] (proteobench.validation.ValidationContext attribute), [1] configure_aggrid() (in module webinterface.pages.base_pages.utils.resulttable) contains() (proteobench.validation.fasta.FastaReference method) (proteobench.validation.FastaReference method) contains_any() (proteobench.validation.fasta.FastaReference method) (proteobench.validation.FastaReference method) contaminant_column (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] contaminant_flag (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] convert_peptidoform() (proteobench.score.denovoscores.DenovoScores method) convert_replicate_to_raw() (proteobench.score.QuantScoresHYE static method) (proteobench.score.quantscoresHYE.QuantScoresHYE static method) convert_to_proforma() (proteobench.io.parsing.parse_settings.ParseModificationSettings method) convert_to_standard_format() (proteobench.io.parsing.parse_settings.ParseSettingsDeNovo method) (proteobench.io.parsing.parse_settings.ParseSettingsEntrapment method) (proteobench.io.parsing.parse_settings.ParseSettingsQuant method) ConvertStandardFormatError copy_dataframes_for_submission() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) count_chars() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) create_branch() (proteobench.github.gh.GithubProteobotRepo method) create_pmultiqc_report_section() (in module webinterface.pages.base_pages.tabs.tab3_view_single_result) create_pull_request() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) (proteobench.github.gh.GithubProteobotRepo method)

D

DatapointAppendError DatapointBase (class in proteobench.datapoint) (class in proteobench.datapoint.datapoint_base) DatapointGenerationError dataset_folder_exists() (in module proteobench.utils.server_io) dataset_selection_indepth (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) dataset_selector_id_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) DatasetAlreadyExistsOnServerError DDAHCDDeNovoModule (class in proteobench.modules.denovo.denovo_DDA_HCD) DDAQuantIonAstralModule (class in proteobench.modules.quant.quant_lfq_ion_DDA_Astral) DDAQuantIonModuleQExactive (class in proteobench.modules.quant.quant_lfq_ion_DDA_QExactive) DDAQuantPeptidoformModule (class in proteobench.modules.quant.quant_lfq_peptidoform_DDA) decoding_strategy (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) decoy_prefixes (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] DEFAULT_DECOY_PREFIXES (in module proteobench.validation.config) default_evaluation (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) DEFAULT_GROUP_SEPARATORS (in module proteobench.validation.protein_ids) default_level (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) default_val_slider (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) DEFAULT_VALIDATION_PROFILE (in module proteobench.validation.config) DenovoDatapoint (class in proteobench.datapoint.denovo_datapoint) DeNovoModule (class in proteobench.modules.denovo.denovo_base) DeNovoPlotGenerator (class in proteobench.plotting.plot_generator_denovo) DenovoScores (class in proteobench.score.denovoscores) DeNovoUIObjects (class in webinterface.pages.base_pages.denovo) description (proteobench.validation.Check attribute), [1] (proteobench.validation.profiles.Check attribute), [1] (proteobench.validation.profiles.ValidationProfile attribute), [1] (proteobench.validation.ValidationProfile attribute), [1] description_files_md (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) description_input_file_md (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) description_module_md (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) description_radios_md (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) description_results_md (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) description_slider_md (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) description_submission_md (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute)

description_table_md (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) detect_newer_version() (in module proteobench.io.params.alphadia) df_head (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) DIAEntrapmentIonModuleAstral (class in proteobench.modules.entrapment.entrapment_ion_DIA_Astral) DIAQuantIonModuleAIF (class in proteobench.modules.quant.quant_lfq_ion_DIA_AIF) DIAQuantIonModuleAstral (class in proteobench.modules.quant.quant_lfq_ion_DIA_Astral) DIAQuantIonModulediaPASEF (class in proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF) DIAQuantIonModulediaSC (class in proteobench.modules.quant.quant_lfq_ion_DIA_singlecell) DIAQuantIonModulePlasma (class in proteobench.modules.quant.quant_lfq_ion_DIA_Plasma) DIAQuantIonModuleZenoTOF (class in proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF) DIAQuantPeptidoformModule (class in proteobench.modules.quant.quant_lfq_peptidoform_DIA) display_all_data_results_main() (webinterface.pages.base_pages.base.BaseUIModule method) (webinterface.pages.base_pages.denovo.DeNovoUIObjects method) (webinterface.pages.base_pages.entrapment.EntrapmentUIObjects method) (webinterface.pages.base_pages.quant.QuantUIObjects method) display_all_data_results_submitted() (webinterface.pages.base_pages.base.BaseUIModule method) (webinterface.pages.base_pages.denovo.DeNovoUIObjects method) (webinterface.pages.base_pages.entrapment.EntrapmentUIObjects method) (webinterface.pages.base_pages.quant.QuantUIObjects method) display_banner() (in module webinterface.pages.base_pages.banner) display_colorblindmode_selector() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results) display_download_section() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results) display_error() (in module webinterface.streamlit_utils) display_existing_results() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results) display_in_depth_plots_generic() (in module webinterface.pages.base_pages.tabs.tab3_view_single_result) (in module webinterface.pages.base_pages.tabs_entrapment.tab3_view_single_result) display_indepth_plots() (webinterface.pages.base_pages.base.BaseUIModule method) (webinterface.pages.base_pages.denovo.DeNovoUIObjects method) (webinterface.pages.base_pages.entrapment.EntrapmentUIObjects method) (webinterface.pages.base_pages.quant.QuantUIObjects method) display_metric_calc_approach_selector() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results) display_metric_selector() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results) display_performance_table() (in module webinterface.pages.base_pages.tabs.tab3_view_single_result) (in module webinterface.pages.base_pages.tabs_entrapment.tab3_view_single_result) display_plots_with_layout() (in module webinterface.pages.base_pages.tabs.tab3_view_single_result) (in module webinterface.pages.base_pages.tabs_entrapment.tab3_view_single_result) display_pmultiqc_report() (in module webinterface.pages.base_pages.tabs.tab3_view_single_result) display_public_submission_ui() (webinterface.pages.base_pages.base.BaseUIModule method) (webinterface.pages.base_pages.denovo.DeNovoUIObjects method) (webinterface.pages.base_pages.entrapment.EntrapmentUIObjects method) (webinterface.pages.base_pages.quant.QuantUIObjects method) display_submission_form() (webinterface.pages.base_pages.base.BaseUIModule method) (webinterface.pages.base_pages.denovo.DeNovoUIObjects method) (webinterface.pages.base_pages.entrapment.EntrapmentUIObjects method) (webinterface.pages.base_pages.quant.QuantUIObjects method) display_submitted_results() (in module webinterface.pages.base_pages.tabs.tab4_view_public_and_new_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab4_view_public_and_new_results) display_workflow_comparison() (in module webinterface.pages.base_pages.tabs.tab5_compare_results) (webinterface.pages.base_pages.denovo.DeNovoUIObjects method) (webinterface.pages.base_pages.quant.QuantUIObjects method) doc_url (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.debug_session_state_variables.Variables attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) (webinterface.pages.utils.module_registry.ModuleMetadata attribute) documentation_description (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) (webinterface.pages.utils.module_registry.ModuleMetadata attribute) download_file() (in module proteobench.utils.server_io) download_selector_id_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) dynamic_range_human_plasma (proteobench.datapoint.quant_datapoint.QuantDatapointPYE attribute), [1]

E

enable_match_between_runs (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] EntrapmentDatapoint (class in proteobench.datapoint.entrapment_datapoint) EntrapmentError EntrapmentModule (class in proteobench.modules.entrapment.entrapment_base_module) EntrapmentPlotGenerator (class in proteobench.plotting.plot_generator_entrapment) EntrapmentScores (class in proteobench.score.entrapmentscores) EntrapmentUIObjects (class in webinterface.pages.base_pages.entrapment) enzyme (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] ERROR (proteobench.validation.report.Severity attribute) (proteobench.validation.Severity attribute) errors (proteobench.validation.report.ValidationReport property) (proteobench.validation.ValidationReport property) evaluate_match() (proteobench.score.denovoscores.DenovoScores method) evaluate_ptm() (proteobench.datapoint.denovo_datapoint.DenovoDatapoint static method) evaluation_mode_toggle_tab3_features (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) evaluation_mode_toggle_tab3_species (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) examples (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] execute_proteobench() (in module webinterface.pages.base_pages.tabs.tab2_upload_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab2_upload_results) expected (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] extend() (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationReport method) extend_tuple() (in module proteobench.io.params.maxquant) extend_tuples_with_none() (in module proteobench.io.params.maxquant) extract_calibration_method() (in module proteobench.io.params.spectronaut) extract_cfg_parameter() (in module proteobench.io.params.diann) extract_identifiers() (in module proteobench.validation.protein_ids) extract_mass_tolerance() (in module proteobench.io.params.peaks) (in module proteobench.io.params.spectronaut) extract_modifications() (in module proteobench.io.params.diann)

extract_params() (in module proteobench.io.params.adanovo) (in module proteobench.io.params.alphadia) (in module proteobench.io.params.alphapept) (in module proteobench.io.params.casanovo) (in module proteobench.io.params.contranovo) (in module proteobench.io.params.deepnovo) (in module proteobench.io.params.diann) (in module proteobench.io.params.fragger) (in module proteobench.io.params.i2masschroq) (in module proteobench.io.params.instanovo) (in module proteobench.io.params.maxquant) (in module proteobench.io.params.metamorpheus) (in module proteobench.io.params.msaid) (in module proteobench.io.params.msangel) (in module proteobench.io.params.peaks) (in module proteobench.io.params.pihelixnovo) (in module proteobench.io.params.piprimenovo) (in module proteobench.io.params.pointnovo) (in module proteobench.io.params.proline) (in module proteobench.io.params.quantms) (in module proteobench.io.params.sage) (in module proteobench.io.params.wombat) EXTRACT_PARAMS_DICT (proteobench.modules.denovo.denovo_base.DeNovoModule attribute) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule attribute) (proteobench.modules.quant.quant_base_module.QuantModule attribute) extract_params_mascot_specific() (in module proteobench.io.params.msangel) extract_params_xtandem_specific() (in module proteobench.io.params.msangel) extract_scan_id() (proteobench.io.parsing.parse_settings.ParseSettingsDeNovo method) extract_search_engine() (in module proteobench.io.params.msangel) extract_tolerances() (in module proteobench.io.params.spectronaut) extract_tolerances_with_regex() (in module proteobench.io.params.spectronaut) extract_value() (in module proteobench.io.params.peaks) (in module proteobench.io.params.spectronaut) extract_value_regex() (in module proteobench.io.params.peaks) (in module proteobench.io.params.spectronaut) extract_values_from_nested_lines() (in module proteobench.io.params.alphadia) extract_with_regex() (in module proteobench.io.params.diann) extras (proteobench.validation.context.ValidationContext attribute), [1] (proteobench.validation.ValidationContext attribute), [1]

F

fasta (proteobench.validation.context.ValidationContext attribute), [1] (proteobench.validation.ValidationContext attribute), [1] fasta_filename (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] fasta_url (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] FastaReference (class in proteobench.validation) (class in proteobench.validation.fasta) fdp_curve (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute) field (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] fig_cv (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) fig_logfc (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) fig_ma_plot (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) fig_metric (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) fig_metric_submitted (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) fig_prefix (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute)

fig_ptm_overview (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) fig_ptm_specific (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) fig_species_overview (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) fig_spectrum_feature (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) file_path (webinterface.pages.utils.module_registry.ModuleMetadata attribute) fill_none() (proteobench.io.params.ProteoBenchParameters method) filter_data_if_applicable() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results) filter_data_point() (proteobench.modules.denovo.denovo_base.DeNovoModule static method) (proteobench.modules.quant.quant_base_module.QuantModule static method) filter_data_using_slider() (in module webinterface.pages.base_pages.utils.general) filter_df_numquant_epsilon() (in module proteobench.datapoint.quant_datapoint) filter_df_numquant_nr_feature() (in module proteobench.datapoint.quant_datapoint) filter_modules() (in module webinterface.pages.utils.module_registry) filter_submitted_data_if_applicable() (in module webinterface.pages.base_pages.tabs.tab4_view_public_and_new_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab4_view_public_and_new_results) find_charge() (in module proteobench.io.params.proline) find_cmdline_string() (in module proteobench.io.params.diann) find_min_pep_length() (in module proteobench.io.params.proline) first_new_plot (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) flatten_dict_of_dicts() (in module proteobench.io.params.maxquant) flatten_results_column() (in module proteobench.plotting.plot_generator_denovo) format_scores() (proteobench.io.parsing.parse_settings.ParseSettingsDeNovo method) format_sequence() (proteobench.io.parsing.parse_settings.ParseSettingsDeNovo method) format_tolerances() (in module proteobench.io.params.metamorpheus) fragment_mass_tolerance (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] from_bytes() (proteobench.validation.fasta.FastaReference class method) (proteobench.validation.FastaReference class method) from_identifiers() (proteobench.validation.fasta.FastaReference class method) (proteobench.validation.FastaReference class method) from_parse_settings() (proteobench.validation.config.ModuleValidationConfig class method) (proteobench.validation.ModuleValidationConfig class method) from_path() (proteobench.validation.fasta.FastaReference class method) (proteobench.validation.FastaReference class method) from_text() (proteobench.validation.fasta.FastaReference class method) (proteobench.validation.FastaReference class method) from_url() (proteobench.validation.fasta.FastaReference class method) (proteobench.validation.FastaReference class method) func (proteobench.validation.Check attribute), [1] (proteobench.validation.profiles.Check attribute), [1]

G

generate_additional_parameters_fields() (in module webinterface.pages.base_pages.tabs.tab2_upload_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab2_upload_results) generate_additional_parameters_fields_submission() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) generate_comments_section() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) generate_confirmation_checkbox() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) generate_datapoint() (proteobench.datapoint.datapoint_base.DatapointBase static method) (proteobench.datapoint.DatapointBase static method) (proteobench.datapoint.denovo_datapoint.DenovoDatapoint static method) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint static method) (proteobench.datapoint.quant_datapoint.QuantDatapointHYE static method) (proteobench.datapoint.quant_datapoint.QuantDatapointPYE static method) (proteobench.datapoint.QuantDatapointHYE static method) generate_id() (proteobench.datapoint.datapoint_base.DatapointBase method) (proteobench.datapoint.DatapointBase method) (proteobench.datapoint.denovo_datapoint.DenovoDatapoint method) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint method) (proteobench.datapoint.quant_datapoint.QuantDatapointHYE method) (proteobench.datapoint.QuantDatapointHYE method) generate_in_depth_plots() (proteobench.plotting.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_base.PlotGeneratorBase method) (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) (proteobench.plotting.plot_generator_lfq_HYE.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_lfq_PYE.LFQPYEPlotGenerator method) (proteobench.plotting.PlotGeneratorBase method) generate_indepth_plots() (in module webinterface.pages.base_pages.tabs.tab3_view_single_result) (in module webinterface.pages.base_pages.tabs_entrapment.tab3_view_single_result) generate_input_fields() (in module webinterface.pages.base_pages.tabs.tab2_upload_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab2_upload_results) generate_input_widget() (in module webinterface.pages.base_pages.utils.inputs) generate_intermediate() (proteobench.score.denovoscores.DenovoScores method) (proteobench.score.entrapmentscores.EntrapmentScores method) (proteobench.score.QuantScoresHYE method) (proteobench.score.quantscoresHYE.QuantScoresHYE method) (proteobench.score.quantscoresPYE.QuantScoresPYE method) (proteobench.score.score_base.ScoreBase method) (proteobench.score.ScoreBase method) generate_main_radio() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results) generate_main_selectbox() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results) generate_main_slider() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) generate_metadata_uploader() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) generate_parameter_filters() (in module webinterface.pages.base_pages.utils.parameter_filters) generate_sample_name() (in module webinterface.pages.base_pages.tabs.tab3_view_single_result) (in module webinterface.pages.base_pages.tabs_entrapment.tab3_view_single_result) generate_submission_button() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) generate_submission_ui_elements() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) generate_submitted_selectbox() (in module webinterface.pages.base_pages.tabs.tab4_view_public_and_new_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab4_view_public_and_new_results) generate_submitted_slider() (in module webinterface.pages.base_pages.tabs.tab4_view_public_and_new_results) get_all_modules() (in module webinterface.pages.utils.module_registry) get_base64_image() (in module webinterface.UI_utils) get_cv_metrics() (proteobench.datapoint.quant_datapoint.QuantDatapointHYE static method) (proteobench.datapoint.QuantDatapointHYE static method) get_epsilon_metrics() (proteobench.datapoint.quant_datapoint.QuantDatapointHYE static method) (proteobench.datapoint.QuantDatapointHYE static method) get_error_suggestions() (in module webinterface.streamlit_utils) get_form_values() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) get_homepage_tour_steps() (in module webinterface.pages.base_pages.tour_steps) get_in_depth_plot_descriptions() (proteobench.plotting.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_base.PlotGeneratorBase method) (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) (proteobench.plotting.plot_generator_lfq_HYE.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_lfq_PYE.LFQPYEPlotGenerator method) (proteobench.plotting.PlotGeneratorBase method)

get_in_depth_plot_layout() (proteobench.plotting.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_base.PlotGeneratorBase method) (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) (proteobench.plotting.plot_generator_lfq_HYE.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_lfq_PYE.LFQPYEPlotGenerator method) (proteobench.plotting.PlotGeneratorBase method) get_incomplete_upload_warning() (in module proteobench.io.params.metamorpheus) get_indepth_metrics() (proteobench.datapoint.denovo_datapoint.DenovoDatapoint method) get_items_between() (in module proteobench.io.params.peaks) get_length_peptidoform_with_nterm() (proteobench.io.parsing.parse_settings.ParseSettingsDeNovo method) get_merged_json() (in module proteobench.utils.server_io) get_metrics() (proteobench.datapoint.datapoint_base.DatapointBase static method) (proteobench.datapoint.DatapointBase static method) (proteobench.datapoint.denovo_datapoint.DenovoDatapoint method) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint static method) (proteobench.datapoint.quant_datapoint.QuantDatapointHYE static method) (proteobench.datapoint.QuantDatapointHYE static method) get_modification_scores() (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator static method) get_module_submission_data() (in module webinterface.UI_utils) get_monthly_visits() (in module webinterface.UI_utils) get_n_modules() (in module webinterface.UI_utils) get_n_modules_proposed() (in module webinterface.UI_utils) get_n_submitted_points() (in module webinterface.UI_utils) get_n_supported_tools() (in module webinterface.UI_utils) get_open_source_tools() (in module proteobench.io.parsing.parse_settings) get_plot_generator() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.entrapment.entrapment_ion_DIA_Astral.DIAEntrapmentIonModuleAstral method) (proteobench.modules.quant.quant_base_module.QuantModule method) (proteobench.modules.quant.quant_lfq_ion_DDA_Astral.DDAQuantIonAstralModule method) (proteobench.modules.quant.quant_lfq_ion_DDA_QExactive.DDAQuantIonModuleQExactive method) (proteobench.modules.quant.quant_lfq_ion_DIA_AIF.DIAQuantIonModuleAIF method) (proteobench.modules.quant.quant_lfq_ion_DIA_Astral.DIAQuantIonModuleAstral method) (proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF.DIAQuantIonModulediaPASEF method) (proteobench.modules.quant.quant_lfq_ion_DIA_Plasma.DIAQuantIonModulePlasma method) (proteobench.modules.quant.quant_lfq_ion_DIA_singlecell.DIAQuantIonModulediaSC method) (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule method) (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule method) get_prc_curve() (in module proteobench.datapoint.denovo_datapoint) get_precision_metrics() (proteobench.datapoint.quant_datapoint.QuantDatapointHYE static method) (proteobench.datapoint.QuantDatapointHYE static method) get_profile() (in module proteobench.validation) (in module proteobench.validation.profiles) get_proforma_bracketed() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) get_ptm_metrics() (proteobench.datapoint.denovo_datapoint.DenovoDatapoint method) get_quant_tour_steps() (in module webinterface.pages.base_pages.tour_steps) get_raw_data() (in module proteobench.utils.server_io) get_remote_url_anon() (proteobench.github.gh.GithubProteobotRepo method) get_species_metrics() (proteobench.datapoint.denovo_datapoint.DenovoDatapoint method) get_spectrum_metrics() (proteobench.datapoint.denovo_datapoint.DenovoDatapoint method) get_stripped_seq() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) get_submission_dict() (in module proteobench.utils.submission) get_submission_source() (in module proteobench.github.gh) get_tab_config() (webinterface.pages.7_denovo_DDA_HCD.StreamlitUI method) (webinterface.pages.base.BaseStreamlitUI method) get_token_mass() (proteobench.score.denovoscores.DenovoScores method) get_token_str() (proteobench.score.denovoscores.DenovoScores method) get_tour_steps() (webinterface.pages.base_pages.base.BaseUIModule method) (webinterface.pages.base_pages.quant.QuantUIObjects method) get_upload_info() (proteobench.io.parsing.parse_settings.ParseSettingsBuilder method) github_link_pr (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) GithubProteobotRepo (class in proteobench.github.gh)

H

handle_benchmarking_error() (in module proteobench.modules.quant.benchmarking) has_errors (proteobench.validation.report.ValidationReport property) (proteobench.validation.ValidationReport property) hide_streamlit_menu() (in module webinterface.streamlit_utils) highlight_list (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute)

highlight_list_submitted (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) homogenize_modification_string() (in module proteobench.io.params.alphadia)

I

id (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] ident_fdr_peptide (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] ident_fdr_protein (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] ident_fdr_psm (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] identifiers (proteobench.validation.fasta.FastaReference property) (proteobench.validation.FastaReference property) identify_file_type() (in module proteobench.io.params.metamorpheus) INFO (proteobench.validation.report.Severity attribute) (proteobench.validation.Severity attribute) infos (proteobench.validation.report.ValidationReport property) (proteobench.validation.ValidationReport property) initial_parameters (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) initial_results (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) initialize_default_parameters() (in module proteobench.io.params.alphadia) initialize_main_data_points() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs.tab2_upload_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab2_upload_results) initialize_main_selectbox() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results) initialize_main_slider() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) initialize_radio() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results) initialize_submitted_data_points() (in module webinterface.pages.base_pages.tabs.tab4_view_public_and_new_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab4_view_public_and_new_results) initialize_submitted_slider() (in module webinterface.pages.base_pages.tabs.tab4_view_public_and_new_results) initialize_uuid_state() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs.tab4_view_public_and_new_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab4_view_public_and_new_results) input_df (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute)

input_df_submission (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) input_file (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute) input_format (proteobench.validation.context.ValidationContext attribute), [1] (proteobench.validation.ValidationContext attribute), [1] (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute) intermediate_hash (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] IntermediateFormatGenerationError is_debug_enabled() (in module webinterface.pages.utils.module_registry) is_decoy_or_contaminant() (in module proteobench.validation.protein_ids) is_implemented() (in module proteobench.modules.rescoring.module_rescoring) (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.denovo.denovo_DDA_HCD.DDAHCDDeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.entrapment.entrapment_ion_DIA_Astral.DIAEntrapmentIonModuleAstral method) (proteobench.modules.quant.quant_base_module.QuantModule method) (proteobench.modules.quant.quant_lfq_ion_DDA_Astral.DDAQuantIonAstralModule method) (proteobench.modules.quant.quant_lfq_ion_DDA_QExactive.DDAQuantIonModuleQExactive method) (proteobench.modules.quant.quant_lfq_ion_DIA_AIF.DIAQuantIonModuleAIF method) (proteobench.modules.quant.quant_lfq_ion_DIA_Astral.DIAQuantIonModuleAstral method) (proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF.DIAQuantIonModulediaPASEF method) (proteobench.modules.quant.quant_lfq_ion_DIA_Plasma.DIAQuantIonModulePlasma method) (proteobench.modules.quant.quant_lfq_ion_DIA_singlecell.DIAQuantIonModulediaSC method) (proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF.DIAQuantIonModuleZenoTOF method) (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule method) (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule method) is_official_server() (in module proteobench.github.gh) is_temporary (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] isotope_error_range (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) issues (proteobench.validation.report.ValidationReport attribute), [1] (proteobench.validation.ValidationReport attribute), [1]

K

keep_latest_version_per_tool() (in module webinterface.pages.base_pages.utils.parameter_filters) keywords (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.debug_session_state_variables.Variables attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) (webinterface.pages.utils.module_registry.ModuleMetadata attribute)

L

label (webinterface.pages.utils.module_registry.ModuleMetadata attribute) legal_notice (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) LFQHYEPlotGenerator (class in proteobench.plotting) (class in proteobench.plotting.plot_generator_lfq_HYE) LFQPYEPlotGenerator (class in proteobench.plotting.plot_generator_lfq_PYE) load_files() (in module proteobench.io.params.metamorpheus) (in module proteobench.io.params.quantms) load_input_file() (in module proteobench.io.parsing.parse_denovo) (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform)

load_params_file() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.quant.quant_base_module.QuantModule method) load_parsed_sdrf() (in module proteobench.io.params.quantms) load_public_performance_data() (in module webinterface.pages.base_pages.tabs.tab3_view_single_result) (in module webinterface.pages.base_pages.tabs_entrapment.tab3_view_single_result) load_user_parameters() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) load_versions() (in module proteobench.io.params.quantms) lower_bound_FDP (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1]

M

main_page() (webinterface.pages.base.BaseStreamlitUI method) make_submission() (in module proteobench.utils.server_io) map_keys_to_desired_format() (in module proteobench.io.params.alphadia) mass_diff() (proteobench.score.denovoscores.DenovoScores method) match_brackets() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) max_intensity (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) max_mz (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) max_nr_observed (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) max_peptide_length (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] max_plausible_dalton (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] max_plausible_ppm (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] max_precursor_charge (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) MAX_PROTEIN_EXAMPLES (in module proteobench.validation.checks) MAX_ROW_EXAMPLES (in module proteobench.validation.checks) mean_abs_epsilon (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) mean_abs_epsilon_eq_species (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] mean_abs_epsilon_global (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] mean_abs_epsilon_precision_eq_species (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] mean_abs_epsilon_precision_global (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] median_abs_epsilon (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) median_abs_epsilon_eq_species (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] median_abs_epsilon_global (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] median_abs_epsilon_human_plasma (proteobench.datapoint.quant_datapoint.QuantDatapointPYE attribute), [1] median_abs_epsilon_precision_eq_species (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] median_abs_epsilon_precision_global (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] median_abs_log2_fc_error_spike_ins (proteobench.datapoint.quant_datapoint.QuantDatapointPYE attribute), [1] message (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] meta_data (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) meta_data_file (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute) meta_data_text (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) meta_file_uploader_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) metric_calc_approach_selector_indepth_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) metric_calc_approach_selector_submitted_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) metric_calc_approach_selector_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) metric_plot_labels (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) metric_selector_indepth_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) metric_selector_submitted_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) metric_selector_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) min_intensity (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) min_mz (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) min_peptide_length (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] min_precursor_charge (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) module proteobench proteobench.datapoint proteobench.datapoint.datapoint_base proteobench.datapoint.denovo_datapoint proteobench.datapoint.entrapment_datapoint proteobench.datapoint.quant_datapoint proteobench.exceptions proteobench.github proteobench.github.gh proteobench.io proteobench.io.params proteobench.io.params.adanovo proteobench.io.params.alphadia proteobench.io.params.alphapept proteobench.io.params.casanovo proteobench.io.params.contranovo proteobench.io.params.deepnovo proteobench.io.params.diann proteobench.io.params.fragger proteobench.io.params.i2masschroq proteobench.io.params.instanovo proteobench.io.params.maxquant proteobench.io.params.metamorpheus proteobench.io.params.msaid proteobench.io.params.msangel proteobench.io.params.peaks proteobench.io.params.pihelixnovo proteobench.io.params.piprimenovo proteobench.io.params.pointnovo proteobench.io.params.proline proteobench.io.params.quantms proteobench.io.params.sage proteobench.io.params.spectronaut proteobench.io.params.wombat proteobench.io.parsing proteobench.io.parsing.parse_denovo proteobench.io.parsing.parse_ion proteobench.io.parsing.parse_peptidoform proteobench.io.parsing.parse_settings proteobench.io.parsing.utils proteobench.modules proteobench.modules.constants proteobench.modules.denovo proteobench.modules.denovo.denovo_base proteobench.modules.denovo.denovo_DDA_HCD proteobench.modules.entrapment proteobench.modules.entrapment.entrapment_base_module proteobench.modules.entrapment.entrapment_ion_DIA_Astral proteobench.modules.quant proteobench.modules.quant.benchmarking proteobench.modules.quant.quant_base_module proteobench.modules.quant.quant_lfq_ion_DDA_Astral proteobench.modules.quant.quant_lfq_ion_DDA_QExactive proteobench.modules.quant.quant_lfq_ion_DIA_AIF proteobench.modules.quant.quant_lfq_ion_DIA_Astral proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF proteobench.modules.quant.quant_lfq_ion_DIA_Plasma proteobench.modules.quant.quant_lfq_ion_DIA_singlecell proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF proteobench.modules.quant.quant_lfq_peptidoform_DDA proteobench.modules.quant.quant_lfq_peptidoform_DIA proteobench.modules.rescoring proteobench.modules.rescoring.module_rescoring proteobench.plotting proteobench.plotting.plot_generator_base proteobench.plotting.plot_generator_denovo proteobench.plotting.plot_generator_entrapment proteobench.plotting.plot_generator_lfq_HYE proteobench.plotting.plot_generator_lfq_PYE proteobench.score proteobench.score.denovoscores proteobench.score.entrapmentscores proteobench.score.quantscoresHYE proteobench.score.quantscoresPYE proteobench.score.score_base proteobench.utils proteobench.utils.server_io proteobench.utils.submission proteobench.validation proteobench.validation.checks proteobench.validation.config proteobench.validation.context proteobench.validation.exceptions proteobench.validation.fasta proteobench.validation.profiles proteobench.validation.protein_ids proteobench.validation.report proteobench.validation.validator webinterface webinterface.Home webinterface.pages webinterface.pages.10_Quant_LFQ_DIA_ion_ZenoTOF webinterface.pages.11_Quant_LFQ_DIA_ion_Plasma webinterface.pages.12_Entrapment_DIA_ion_Astral webinterface.pages.2_Quant_LFQ_DDA_ion_QExactive webinterface.pages.3_Quant_LFQ_DIA_ion_AIF webinterface.pages.4_Quant_LFQ_DIA_ion_diaPASEF webinterface.pages.5_Quant_LFQ_DDA_peptidoform webinterface.pages.6_Quant_LFQ_DIA_ion_Astral webinterface.pages.7_denovo_DDA_HCD webinterface.pages.8_Quant_LFQ_DDA_ion_Astral webinterface.pages.9_Quant_LFQ_DIA_ion_singlecell webinterface.pages.base webinterface.pages.base_pages webinterface.pages.base_pages.banner webinterface.pages.base_pages.base webinterface.pages.base_pages.denovo webinterface.pages.base_pages.entrapment webinterface.pages.base_pages.quant webinterface.pages.base_pages.tabs webinterface.pages.base_pages.tabs.tab1_view_public_results webinterface.pages.base_pages.tabs.tab2_upload_results webinterface.pages.base_pages.tabs.tab3_view_single_result webinterface.pages.base_pages.tabs.tab4_view_public_and_new_results webinterface.pages.base_pages.tabs.tab5_compare_results webinterface.pages.base_pages.tabs.tab6_submit_results webinterface.pages.base_pages.tabs_entrapment webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results webinterface.pages.base_pages.tabs_entrapment.tab2_upload_results webinterface.pages.base_pages.tabs_entrapment.tab3_view_single_result webinterface.pages.base_pages.tabs_entrapment.tab4_view_public_and_new_results webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results webinterface.pages.base_pages.tour_steps webinterface.pages.base_pages.utils webinterface.pages.base_pages.utils.general webinterface.pages.base_pages.utils.inputs webinterface.pages.base_pages.utils.metricplot webinterface.pages.base_pages.utils.parameter_filters webinterface.pages.base_pages.utils.resulttable webinterface.pages.base_pages.utils.session_state webinterface.pages.base_pages.utils.validation_ui webinterface.pages.future_pages webinterface.pages.markdown_files webinterface.pages.markdown_files.DeNovo webinterface.pages.markdown_files.DeNovo.DDA webinterface.pages.markdown_files.Entrapment webinterface.pages.markdown_files.Entrapment.DIA webinterface.pages.markdown_files.Entrapment.DIA.ion webinterface.pages.markdown_files.Entrapment.DIA.ion.Astral webinterface.pages.markdown_files.Quant webinterface.pages.markdown_files.Quant.lfq webinterface.pages.markdown_files.Quant.lfq.DDA webinterface.pages.markdown_files.Quant.lfq.DDA.ion webinterface.pages.markdown_files.Quant.lfq.DDA.ion.Astral webinterface.pages.markdown_files.Quant.lfq.DDA.ion.QExactive webinterface.pages.markdown_files.Quant.lfq.DDA.peptidoform webinterface.pages.markdown_files.Quant.lfq.DIA webinterface.pages.markdown_files.Quant.lfq.DIA.ion webinterface.pages.markdown_files.Quant.lfq.DIA.ion.AIF webinterface.pages.markdown_files.Quant.lfq.DIA.ion.Astral webinterface.pages.markdown_files.Quant.lfq.DIA.ion.diaPASEF webinterface.pages.markdown_files.Quant.lfq.DIA.ion.singlecell webinterface.pages.markdown_files.Quant.lfq.DIA.ion.ZenoTOF webinterface.pages.pages_variables webinterface.pages.pages_variables.DeNovo webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables webinterface.pages.pages_variables.Entrapment webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables webinterface.pages.pages_variables.Quant webinterface.pages.pages_variables.Quant.debug_session_state_variables webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables webinterface.pages.texts webinterface.pages.texts.generic_texts webinterface.pages.texts.generic_texts_denovo webinterface.pages.texts.generic_texts_dia webinterface.pages.texts.proteobench_builder webinterface.pages.utils webinterface.pages.utils.module_registry webinterface.streamlit_utils webinterface.UI_utils

module_id (proteobench.modules.denovo.denovo_DDA_HCD.DDAHCDDeNovoModule attribute) (proteobench.modules.entrapment.entrapment_ion_DIA_Astral.DIAEntrapmentIonModuleAstral attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DDA_Astral.DDAQuantIonAstralModule attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DDA_QExactive.DDAQuantIonModuleQExactive attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DIA_AIF.DIAQuantIonModuleAIF attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DIA_Astral.DIAQuantIonModuleAstral attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF.DIAQuantIonModulediaPASEF attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DIA_Plasma.DIAQuantIonModulePlasma attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DIA_singlecell.DIAQuantIonModulediaSC attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF.DIAQuantIonModuleZenoTOF attribute), [1] (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule attribute), [1] (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule attribute), [1] ModuleMetadata (class in webinterface.pages.utils.module_registry) ModuleValidationConfig (class in proteobench.validation) (class in proteobench.validation.config)

N

n_beams (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) n_peaks (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) name (proteobench.io.params.fragger.Parameter attribute) (proteobench.validation.Check attribute), [1] (proteobench.validation.profiles.Check attribute), [1] (proteobench.validation.profiles.ValidationProfile attribute), [1] (proteobench.validation.ValidationProfile attribute), [1] no_results (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute)

normalize() (proteobench.io.params.ProteoBenchParameters method) normalize_dataframe_columns() (in module proteobench.io.params) normalize_enzyme() (in module proteobench.io.params.diann) nr_feature (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] nr_id_features (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] nr_quantified_spike_ins (proteobench.datapoint.quant_datapoint.QuantDatapointPYE attribute), [1]

O

observed (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1]

obtain_all_data_points() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.quant.quant_base_module.QuantModule method)

P

paired_FDP (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] Parameter (class in proteobench.io.params.fragger) parameters (proteobench.validation.context.ValidationContext attribute), [1] (proteobench.validation.ValidationContext attribute), [1] parameters_additional (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) params_file_dict (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) params_json_dict (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) parse_button (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute) parse_cmdline_string() (in module proteobench.io.params.diann) parse_fasta_header() (in module proteobench.validation.fasta) parse_key_value() (in module proteobench.io.params.alphadia) parse_modifications() (in module proteobench.io.params.metamorpheus) parse_params() (in module proteobench.io.params.fragger) parse_phi_report_filters() (in module proteobench.io.params.fragger) parse_predictors_library() (in module proteobench.io.params.diann) parse_protein_inference_method() (in module proteobench.io.params.diann) parse_proteobench_index() (in module webinterface.UI_utils) parse_quantification_strategy() (in module proteobench.io.params.diann) parse_setting() (in module proteobench.io.params.diann) parse_settings_dir (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) parse_version_key() (in module webinterface.pages.base_pages.utils.parameter_filters) ParseError ParseModificationSettings (class in proteobench.io.parsing.parse_settings) ParseSettingsBuilder (class in proteobench.io.parsing.parse_settings) ParseSettingsDeNovo (class in proteobench.io.parsing.parse_settings) ParseSettingsEntrapment (class in proteobench.io.parsing.parse_settings) ParseSettingsError ParseSettingsQuant (class in proteobench.io.parsing.parse_settings) passed (proteobench.validation.report.ValidationReport property) (proteobench.validation.ValidationReport property) path (webinterface.pages.utils.module_registry.ModuleMetadata attribute) placeholder_dataset_selection_container (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) placeholder_downloads_container (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) placeholder_fig_compare (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) placeholder_slider (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) placeholder_slider_submitted (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) placeholder_table (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) placeholder_table_submitted (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) plot_category_strip() (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) plot_fdp_id_scatter() (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) plot_fdp_ratio() (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) plot_forest() (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) plot_main_metric() (proteobench.plotting.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_base.PlotGeneratorBase method) (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) (proteobench.plotting.plot_generator_lfq_HYE.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_lfq_PYE.LFQPYEPlotGenerator method) (proteobench.plotting.PlotGeneratorBase method) plot_ptm_overview() (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) plot_ptm_specific() (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) plot_species_overview() (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) plot_species_specific() (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) plot_spectrum_feature() (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) PlotError PlotGeneratorBase (class in proteobench.plotting) (class in proteobench.plotting.plot_generator_base) precision_aa (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) precision_peptide (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) precursor_column_name (proteobench.modules.entrapment.entrapment_ion_DIA_Astral.DIAEntrapmentIonModuleAstral attribute) (proteobench.modules.quant.quant_lfq_ion_DDA_Astral.DDAQuantIonAstralModule attribute) (proteobench.modules.quant.quant_lfq_ion_DDA_QExactive.DDAQuantIonModuleQExactive attribute) (proteobench.modules.quant.quant_lfq_ion_DIA_AIF.DIAQuantIonModuleAIF attribute) (proteobench.modules.quant.quant_lfq_ion_DIA_Astral.DIAQuantIonModuleAstral attribute) (proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF.DIAQuantIonModulediaPASEF attribute) (proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF.DIAQuantIonModuleZenoTOF attribute) (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule attribute) (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule attribute) precursor_mass_tolerance (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] precursor_name (proteobench.modules.quant.quant_lfq_ion_DIA_Plasma.DIAQuantIonModulePlasma attribute) (proteobench.modules.quant.quant_lfq_ion_DIA_singlecell.DIAQuantIonModulediaSC attribute) prefix_params (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) prepare_display_dataframe() (in module webinterface.pages.base_pages.utils.resulttable) privacy_notice (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) process_fragment_mz() (in module proteobench.io.params.alphadia) process_key_value_line() (in module proteobench.io.params.alphadia) process_precursor_charge() (in module proteobench.io.params.alphadia) process_precursor_len() (in module proteobench.io.params.alphadia) process_precursor_mz() (in module proteobench.io.params.alphadia)

process_submission_form() (in module webinterface.pages.base_pages.tabs.tab2_upload_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab2_upload_results) proforma_column (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] protein_column (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] protein_group_separators (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] proteobench module proteobench.datapoint module proteobench.datapoint.datapoint_base module proteobench.datapoint.denovo_datapoint module proteobench.datapoint.entrapment_datapoint module proteobench.datapoint.quant_datapoint module proteobench.exceptions module proteobench.github module proteobench.github.gh module proteobench.io module proteobench.io.params module proteobench.io.params.adanovo module proteobench.io.params.alphadia module proteobench.io.params.alphapept module proteobench.io.params.casanovo module proteobench.io.params.contranovo module proteobench.io.params.deepnovo module proteobench.io.params.diann module proteobench.io.params.fragger module proteobench.io.params.i2masschroq module proteobench.io.params.instanovo module proteobench.io.params.maxquant module proteobench.io.params.metamorpheus module proteobench.io.params.msaid module proteobench.io.params.msangel module proteobench.io.params.peaks module proteobench.io.params.pihelixnovo module proteobench.io.params.piprimenovo module proteobench.io.params.pointnovo module proteobench.io.params.proline module proteobench.io.params.quantms module proteobench.io.params.sage module proteobench.io.params.spectronaut module proteobench.io.params.wombat module proteobench.io.parsing module proteobench.io.parsing.parse_denovo module proteobench.io.parsing.parse_ion module proteobench.io.parsing.parse_peptidoform module proteobench.io.parsing.parse_settings module proteobench.io.parsing.utils module proteobench.modules module proteobench.modules.constants module proteobench.modules.denovo module proteobench.modules.denovo.denovo_base module proteobench.modules.denovo.denovo_DDA_HCD module proteobench.modules.entrapment module proteobench.modules.entrapment.entrapment_base_module module proteobench.modules.entrapment.entrapment_ion_DIA_Astral module proteobench.modules.quant module proteobench.modules.quant.benchmarking module proteobench.modules.quant.quant_base_module module proteobench.modules.quant.quant_lfq_ion_DDA_Astral module proteobench.modules.quant.quant_lfq_ion_DDA_QExactive module proteobench.modules.quant.quant_lfq_ion_DIA_AIF module proteobench.modules.quant.quant_lfq_ion_DIA_Astral module proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF module proteobench.modules.quant.quant_lfq_ion_DIA_Plasma module proteobench.modules.quant.quant_lfq_ion_DIA_singlecell module proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF module proteobench.modules.quant.quant_lfq_peptidoform_DDA module proteobench.modules.quant.quant_lfq_peptidoform_DIA module proteobench.modules.rescoring module proteobench.modules.rescoring.module_rescoring module proteobench.plotting module proteobench.plotting.plot_generator_base module proteobench.plotting.plot_generator_denovo module proteobench.plotting.plot_generator_entrapment module proteobench.plotting.plot_generator_lfq_HYE module proteobench.plotting.plot_generator_lfq_PYE module proteobench.score module proteobench.score.denovoscores module proteobench.score.entrapmentscores module proteobench.score.quantscoresHYE module proteobench.score.quantscoresPYE module proteobench.score.score_base module proteobench.utils module proteobench.utils.server_io module proteobench.utils.submission module proteobench.validation module proteobench.validation.checks module proteobench.validation.config module proteobench.validation.context module proteobench.validation.exceptions module proteobench.validation.fasta module proteobench.validation.profiles module proteobench.validation.protein_ids module proteobench.validation.report module proteobench.validation.validator module proteobench_page_config() (in module webinterface.pages.texts.proteobench_builder) proteobench_sidebar() (in module webinterface.pages.texts.proteobench_builder) proteobench_version (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] ProteoBenchError ProteobenchError ProteoBenchParameters (class in proteobench.io.params) ptm_overview (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Description attribute) ptm_specific (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Description attribute) pull_req (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute)

Q

QuantDatapointHYE (class in proteobench.datapoint) (class in proteobench.datapoint.quant_datapoint) QuantDatapointPYE (class in proteobench.datapoint.quant_datapoint) QuantificationError

QuantModule (class in proteobench.modules.quant.quant_base_module) QuantScoresHYE (class in proteobench.score) (class in proteobench.score.quantscoresHYE) QuantScoresPYE (class in proteobench.score.quantscoresPYE) QuantUIObjects (class in webinterface.pages.base_pages.quant)

R

radio_evaluation (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) radio_evaluation_id_indepth_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) radio_evaluation_id_submitted_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) radio_evaluation_id_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) radio_level (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) radio_level_id_indepth_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) radio_level_id_submitted_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) radio_level_id_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) raise_if_errors() (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationReport method) read_file() (in module proteobench.io.params.maxquant) read_file_lines() (in module proteobench.io.params.alphadia) read_fragpipe_workflow() (in module proteobench.io.params.fragger) read_reference_database() (proteobench.validation.config.ModuleValidationConfig static method) (proteobench.validation.ModuleValidationConfig static method) read_results_json_repo() (proteobench.github.gh.GithubProteobotRepo method) read_results_json_repo_single_file() (proteobench.github.gh.GithubProteobotRepo method) read_spectronaut_settings() (in module proteobench.io.params.spectronaut) read_xml_record() (in module proteobench.io.params.maxquant) recall_aa (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) recall_peptide (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) recommended_max_fdr_psm (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] record_proportions_to_results_feature() (proteobench.datapoint.denovo_datapoint.DenovoDatapoint static method) reference (proteobench.validation.context.ValidationContext attribute), [1] (proteobench.validation.ValidationContext attribute), [1] register_profile() (in module proteobench.validation) (in module proteobench.validation.profiles) release_stage (webinterface.pages.utils.module_registry.ModuleMetadata attribute) remove_precursor_tol (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) render_aggrid() (in module webinterface.pages.base_pages.utils.resulttable) render_links() (in module webinterface.pages.texts.proteobench_builder) render_main_plot() (in module webinterface.pages.base_pages.tabs.tab1_view_public_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results) render_metric_plot() (in module webinterface.pages.base_pages.utils.metricplot) render_plot_options_expander() (webinterface.pages.base_pages.base.BaseUIModule method) render_results_table() (in module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results) render_submitted_results_table() (in module webinterface.pages.base_pages.tabs.tab4_view_public_and_new_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab4_view_public_and_new_results) render_validation_report() (in module webinterface.pages.base_pages.utils.validation_ui) reported_fdr_parsed_from_input (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] result_perf (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute)

result_performance_submission (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) result_plot_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) result_submitted_plot_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) results (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] results_repo (webinterface.pages.utils.module_registry.ModuleMetadata attribute) run() (proteobench.validation.Check method) (proteobench.validation.profiles.Check method) run_benchmarking() (in module proteobench.modules.quant.benchmarking) run_benchmarking_process() (in module webinterface.pages.base_pages.tabs.tab2_upload_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab2_upload_results) run_benchmarking_with_timing() (in module proteobench.modules.quant.benchmarking) run_instructions (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) run_submission_validation() (in module webinterface.pages.base_pages.utils.validation_ui)

S

save_dataframe() (in module webinterface.streamlit_utils) save_intermediate_submission_data() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) ScoreBase (class in proteobench.score) (class in proteobench.score.score_base) search_engine (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] search_engine_version (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] selectbox_id_indepth_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) selectbox_id_submitted_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) selectbox_id_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) sequence_column (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] set_highlight_column_in_submitted_data() (in module webinterface.pages.base_pages.tabs.tab2_upload_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab2_upload_results) Severity (class in proteobench.validation) (class in proteobench.validation.report) severity (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] shallow_clone() (proteobench.github.gh.GithubProteobotRepo static method) show_download_button() (in module webinterface.pages.base_pages.tabs.tab3_view_single_result) show_software_selector_and_alphadia_info() (in module webinterface.pages.base_pages.tabs.tab2_upload_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab2_upload_results) show_submission_success_message() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) sidebar_category (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.debug_session_state_variables.Variables attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) sidebar_label (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.debug_session_state_variables.Variables attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) sidebar_path (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.debug_session_state_variables.Variables attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute)

slider_id_indepth_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) slider_id_submitted_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) slider_id_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) software_name (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] software_version (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] species (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Description attribute) species_dict() (proteobench.io.parsing.parse_settings.ParseSettingsQuant method) species_expected_ratio() (proteobench.io.parsing.parse_settings.ParseSettingsQuant method) species_flags (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] spectrum_features_overview (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Description attribute) split_protein_groups() (in module proteobench.validation.protein_ids) standard_df (proteobench.validation.context.ValidationContext attribute), [1] (proteobench.validation.ValidationContext attribute), [1] stat_box() (in module webinterface.UI_utils) store_submission_keyword() (in module webinterface.pages.base_pages.tabs.tab2_upload_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab2_upload_results) StreamlitLogger (class in webinterface.streamlit_utils) StreamlitPageHome (class in webinterface.Home) StreamlitUI (class in webinterface.pages.11_Quant_LFQ_DIA_ion_Plasma) (class in webinterface.pages.12_Entrapment_DIA_ion_Astral) (class in webinterface.pages.7_denovo_DDA_HCD) submission_processing_warning (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) submission_result_description (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) SubmissionValidationError, [1] submit (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) submit_to_repository() (in module webinterface.pages.base_pages.tabs.tab6_submit_results) (in module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results) summary() (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationReport method)

T

table_id_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) table_new_results_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) texts (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute)

title (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.debug_session_state_variables.Variables attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) (webinterface.pages.utils.module_registry.ModuleMetadata attribute) to_dict() (proteobench.validation.report.ValidationIssue method) (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationIssue method) (proteobench.validation.ValidationReport method) to_lowercase() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) tokens (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute)

U

ui_key_inspector() (in module webinterface.pages.base_pages.utils.session_state) ui_overview_table() (in module webinterface.pages.base_pages.utils.session_state) unregister_profile() (in module proteobench.validation) (in module proteobench.validation.profiles)

update_parameters_submission_form() (in module webinterface.pages.base_pages.utils.inputs) uploaded_id (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute)

V

validate_entrapment_coverage() (proteobench.score.entrapmentscores.EntrapmentScores static method) VALIDATE_FILES_DICT (proteobench.modules.quant.quant_base_module.QuantModule attribute) validate_params_files() (proteobench.modules.quant.quant_base_module.QuantModule method) validate_submission() (in module proteobench.validation) (in module proteobench.validation.validator) validation_profile (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] ValidationContext (class in proteobench.validation) (class in proteobench.validation.context) ValidationError ValidationIssue (class in proteobench.validation) (class in proteobench.validation.report) ValidationProfile (class in proteobench.validation) (class in proteobench.validation.profiles)

ValidationReport (class in proteobench.validation) (class in proteobench.validation.report) value (proteobench.io.params.fragger.Parameter attribute) Variables (class in webinterface.pages.pages_variables.Quant.debug_session_state_variables) VariablesDDADeNovo (class in webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables) VariablesDDAQuant (class in webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables) (class in webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables) VariablesDDAQuantAstral (class in webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables) VariablesDIAEntrapmentAstral (class in webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables) VariablesDIAQuant (class in webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables) VariablesDIAQuantAstral (class in webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables) VariablesDIAQuantdiaPASEF (class in webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables) VariablesDIAQuantPlasma (class in webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables) VariablesDIAQuantSC (class in webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables) VariablesDIAQuantZenoTOF (class in webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables)

W

WARNING (proteobench.validation.report.Severity attribute) (proteobench.validation.Severity attribute) warning_alpha (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) warning_archived (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) warning_beta (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) warnings (proteobench.validation.report.ValidationReport property) (proteobench.validation.ValidationReport property) webinterface module webinterface.Home module webinterface.pages module webinterface.pages.10_Quant_LFQ_DIA_ion_ZenoTOF module webinterface.pages.11_Quant_LFQ_DIA_ion_Plasma module webinterface.pages.12_Entrapment_DIA_ion_Astral module webinterface.pages.2_Quant_LFQ_DDA_ion_QExactive module webinterface.pages.3_Quant_LFQ_DIA_ion_AIF module webinterface.pages.4_Quant_LFQ_DIA_ion_diaPASEF module webinterface.pages.5_Quant_LFQ_DDA_peptidoform module webinterface.pages.6_Quant_LFQ_DIA_ion_Astral module webinterface.pages.7_denovo_DDA_HCD module webinterface.pages.8_Quant_LFQ_DDA_ion_Astral module webinterface.pages.9_Quant_LFQ_DIA_ion_singlecell module webinterface.pages.base module webinterface.pages.base_pages module webinterface.pages.base_pages.banner module webinterface.pages.base_pages.base module webinterface.pages.base_pages.denovo module webinterface.pages.base_pages.entrapment module webinterface.pages.base_pages.quant module webinterface.pages.base_pages.tabs module webinterface.pages.base_pages.tabs.tab1_view_public_results module webinterface.pages.base_pages.tabs.tab2_upload_results module webinterface.pages.base_pages.tabs.tab3_view_single_result module webinterface.pages.base_pages.tabs.tab4_view_public_and_new_results module webinterface.pages.base_pages.tabs.tab5_compare_results module webinterface.pages.base_pages.tabs.tab6_submit_results module webinterface.pages.base_pages.tabs_entrapment module webinterface.pages.base_pages.tabs_entrapment.tab1_view_public_results module webinterface.pages.base_pages.tabs_entrapment.tab2_upload_results module webinterface.pages.base_pages.tabs_entrapment.tab3_view_single_result module webinterface.pages.base_pages.tabs_entrapment.tab4_view_public_and_new_results module webinterface.pages.base_pages.tabs_entrapment.tab6_submit_results module webinterface.pages.base_pages.tour_steps module webinterface.pages.base_pages.utils module webinterface.pages.base_pages.utils.general module webinterface.pages.base_pages.utils.inputs module webinterface.pages.base_pages.utils.metricplot module webinterface.pages.base_pages.utils.parameter_filters module webinterface.pages.base_pages.utils.resulttable module webinterface.pages.base_pages.utils.session_state module webinterface.pages.base_pages.utils.validation_ui module webinterface.pages.future_pages module webinterface.pages.markdown_files module webinterface.pages.markdown_files.DeNovo module

webinterface.pages.markdown_files.DeNovo.DDA module webinterface.pages.markdown_files.Entrapment module webinterface.pages.markdown_files.Entrapment.DIA module webinterface.pages.markdown_files.Entrapment.DIA.ion module webinterface.pages.markdown_files.Entrapment.DIA.ion.Astral module webinterface.pages.markdown_files.Quant module webinterface.pages.markdown_files.Quant.lfq module webinterface.pages.markdown_files.Quant.lfq.DDA module webinterface.pages.markdown_files.Quant.lfq.DDA.ion module webinterface.pages.markdown_files.Quant.lfq.DDA.ion.Astral module webinterface.pages.markdown_files.Quant.lfq.DDA.ion.QExactive module webinterface.pages.markdown_files.Quant.lfq.DDA.peptidoform module webinterface.pages.markdown_files.Quant.lfq.DIA module webinterface.pages.markdown_files.Quant.lfq.DIA.ion module webinterface.pages.markdown_files.Quant.lfq.DIA.ion.AIF module webinterface.pages.markdown_files.Quant.lfq.DIA.ion.Astral module webinterface.pages.markdown_files.Quant.lfq.DIA.ion.diaPASEF module webinterface.pages.markdown_files.Quant.lfq.DIA.ion.singlecell module webinterface.pages.markdown_files.Quant.lfq.DIA.ion.ZenoTOF module webinterface.pages.pages_variables module webinterface.pages.pages_variables.DeNovo module webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables module webinterface.pages.pages_variables.Entrapment module webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables module webinterface.pages.pages_variables.Quant module webinterface.pages.pages_variables.Quant.debug_session_state_variables module webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables module webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables module webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables module webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables module webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables module webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables module webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables module webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables module webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables module webinterface.pages.texts module webinterface.pages.texts.generic_texts module webinterface.pages.texts.generic_texts_denovo module webinterface.pages.texts.generic_texts_dia module webinterface.pages.texts.proteobench_builder module webinterface.pages.utils module webinterface.pages.utils.module_registry module webinterface.streamlit_utils module webinterface.UI_utils module WebpageTexts (class in webinterface.pages.texts.generic_texts) (class in webinterface.pages.texts.generic_texts_denovo) (class in webinterface.pages.texts.generic_texts_dia) WebpageTexts.Description (class in webinterface.pages.texts.generic_texts_denovo) WebpageTexts.Help (class in webinterface.pages.texts.generic_texts) (class in webinterface.pages.texts.generic_texts_denovo) (class in webinterface.pages.texts.generic_texts_dia) WebpageTexts.ShortMessages (class in webinterface.pages.texts.generic_texts) (class in webinterface.pages.texts.generic_texts_denovo) (class in webinterface.pages.texts.generic_texts_dia) write_intermediate_raw() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.quant.quant_base_module.QuantModule method) write_json_local_development() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.quant.quant_base_module.QuantModule method)

Y

y_axis_title (proteobench.modules.quant.quant_base_module.QuantModule attribute) (proteobench.modules.quant.quant_lfq_ion_DIA_Plasma.DIAQuantIonModulePlasma attribute) (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule attribute) (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables.VariablesDIAQuantSC attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute)