Index

A

add_current_data_point() (proteobench.modules.quant.quant_base_module.QuantModule method) add_fixed_mod() (in module proteobench.io.parsing.utils) add_maxquant_fixed_modifications() (in module proteobench.io.parsing.utils) add_modification_parser() (proteobench.io.parsing.parse_settings.ParseSettingsQuant method) add_record() (in module proteobench.io.params.maxquant) additional_params_json (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) 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.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)

all_datapoints_submission (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) all_datapoints_submitted (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) allowed_miscleavages (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1]

B

benchmarking() (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.DIAQuantIonModule 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_singlecell.DIAQuantIonModulediaSC method) (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule method) (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule method) beta_warning (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)

build_parser() (proteobench.io.parsing.parse_settings.ParseSettingsBuilder method) build_Series_from_records() (in module proteobench.io.params.maxquant) button_submission_uuid (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)

C

check_new_unique_hash() (proteobench.modules.quant.quant_base_module.QuantModule method) check_submission (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) check_submission_uuid (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) 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() (webinterface.pages.base_pages.quant.QuantUIObjects method) clone() (proteobench.github.gh.GithubProteobotRepo static method) clone_pr() (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) comment (proteobench.io.params.fragger.Parameter attribute) comments (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] comments_submission_uuid (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) commit() (proteobench.github.gh.GithubProteobotRepo method) compare_dictionaries() (in module webinterface.pages.base_pages.quant) compute_condition_stats() (proteobench.score.quant.quantscores.QuantScores static method) compute_epsilon() (proteobench.score.quant.quantscores.QuantScores static method) convert_replicate_to_raw() (proteobench.score.quant.quantscores.QuantScores static method) convert_to_proforma() (proteobench.io.parsing.parse_settings.ParseModificationSettings method) convert_to_standard_format() (proteobench.io.parsing.parse_settings.ParseSettingsQuant method) ConvertStandardFormatError copy_dataframes_for_submission() (webinterface.pages.base_pages.quant.QuantUIObjects method) count_chars() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) create_branch() (proteobench.github.gh.GithubProteobotRepo method) create_pull_request() (proteobench.github.gh.GithubProteobotRepo method) (webinterface.pages.base_pages.quant.QuantUIObjects method)

D

DatapointAppendError DatapointGenerationError dataset_selector_id_uuid (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) 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) default_val_slider (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) description_files_md (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) description_input_file_md (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) description_module_md (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) description_results_md (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) description_slider_md (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)

description_submission_md (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) description_table_md (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) df_head (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) DIAQuantIonModule (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) DIAQuantPeptidoformModule (class in proteobench.modules.quant.quant_lfq_peptidoform_DIA) display_all_data_results_main() (webinterface.pages.base_pages.quant.QuantUIObjects method) display_all_data_results_submitted() (webinterface.pages.base_pages.quant.QuantUIObjects method) display_download_section() (webinterface.pages.base_pages.quant.QuantUIObjects method) display_existing_results() (webinterface.pages.base_pages.quant.QuantUIObjects method) display_indepth_plots() (webinterface.pages.base_pages.quant.QuantUIObjects method) display_public_submission_ui() (webinterface.pages.base_pages.quant.QuantUIObjects method) display_submission_form() (webinterface.pages.base_pages.quant.QuantUIObjects method) display_submitted_results() (webinterface.pages.base_pages.quant.QuantUIObjects method) doc_url (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) download_selector_id_uuid (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)

E

enable_match_between_runs (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] enzyme (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] execute_proteobench() (webinterface.pages.base_pages.quant.QuantUIObjects 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_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.alphadia) (in module proteobench.io.params.alphapept) (in module proteobench.io.params.diann) (in module proteobench.io.params.fragger) (in module proteobench.io.params.i2masschroq) (in module proteobench.io.params.maxquant) (in module proteobench.io.params.msaid) (in module proteobench.io.params.msangel) (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.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_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)

F

fig_cv (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) fig_logfc (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) fig_ma_plot (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) fig_metric (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)

fill_none() (proteobench.io.params.ProteoBenchParameters method) filter_data_main_slider() (webinterface.pages.base_pages.quant.QuantUIObjects method) filter_data_point() (proteobench.modules.quant.quant_base_module.QuantModule static method) filter_data_submitted_slider() (webinterface.pages.base_pages.quant.QuantUIObjects method) filter_df_numquant_epsilon() (in module proteobench.datapoint.quant_datapoint) filter_df_numquant_nr_prec() (in module proteobench.datapoint.quant_datapoint) 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.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) flatten_dict_of_dicts() (in module proteobench.io.params.maxquant) fragment_mass_tolerance (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1]

G

generate_additional_parameters_fields() (webinterface.pages.base_pages.quant.QuantUIObjects method) generate_additional_parameters_fields_submission() (webinterface.pages.base_pages.quant.QuantUIObjects method) generate_comments_section() (webinterface.pages.base_pages.quant.QuantUIObjects method) generate_confirmation_checkbox() (webinterface.pages.base_pages.quant.QuantUIObjects method) generate_datapoint() (proteobench.datapoint.quant_datapoint.QuantDatapoint static method) generate_id() (proteobench.datapoint.quant_datapoint.QuantDatapoint method) generate_indepth_plots() (webinterface.pages.base_pages.quant.QuantUIObjects method) generate_input_fields() (webinterface.pages.base_pages.quant.QuantUIObjects method) generate_input_widget() (webinterface.pages.base_pages.quant.QuantUIObjects method) generate_intermediate() (proteobench.score.quant.quantscores.QuantScores method) generate_main_selectbox() (webinterface.pages.base_pages.quant.QuantUIObjects method) generate_main_slider() (webinterface.pages.base_pages.quant.QuantUIObjects method) generate_metadata_uploader() (webinterface.pages.base_pages.quant.QuantUIObjects method) generate_sample_name() (webinterface.pages.base_pages.quant.QuantUIObjects method) generate_submission_button() (webinterface.pages.base_pages.quant.QuantUIObjects method) generate_submission_ui_elements() (webinterface.pages.base_pages.quant.QuantUIObjects method) generate_submitted_selectbox() (webinterface.pages.base_pages.quant.QuantUIObjects method) generate_submitted_slider() (webinterface.pages.base_pages.quant.QuantUIObjects method)

generate_text_area_widget() (webinterface.pages.base_pages.quant.QuantUIObjects method) get_form_values() (webinterface.pages.base_pages.quant.QuantUIObjects method) get_items_between() (in module proteobench.io.params.peaks) get_metrics() (proteobench.datapoint.quant_datapoint.QuantDatapoint static method) get_proforma_bracketed() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) get_remote_url_anon() (proteobench.github.gh.GithubProteobotRepo 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) github_link_pr (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) GithubProteobotRepo (class in proteobench.github.gh)

H

handle_submitted_table_edits() (webinterface.pages.base_pages.quant.QuantUIObjects method) hide_streamlit_menu() (in module webinterface.streamlit_utils) highlight_list (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)

highlight_list_submitted (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)

I

id (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] ident_fdr_peptide (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] ident_fdr_protein (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] ident_fdr_psm (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] initial_parameters (webinterface.pages.texts.generic_texts.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_dia.WebpageTexts.ShortMessages attribute) initialize_default_parameters() (in module proteobench.io.params.alphadia) initialize_main_data_points() (webinterface.pages.base_pages.quant.QuantUIObjects method) initialize_main_slider() (webinterface.pages.base_pages.quant.QuantUIObjects method) initialize_submitted_data_points() (webinterface.pages.base_pages.quant.QuantUIObjects method) initialize_submitted_slider() (webinterface.pages.base_pages.quant.QuantUIObjects method) input_df (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) input_df_submission (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)

input_file (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute) input_format (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute) intermediate_hash (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] IntermediateFormatGenerationError is_implemented() (in module proteobench.modules.rescoring.module_rescoring) (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.DIAQuantIonModule 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_singlecell.DIAQuantIonModulediaSC method) (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule method) (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule method) is_temporary (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1]

L

legal_notice (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) load_files() (in module proteobench.io.params.quantms) load_input_file() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform)

load_params_file() (proteobench.modules.quant.quant_base_module.QuantModule method) load_parsed_sdrf() (in module proteobench.io.params.quantms) load_user_parameters() (webinterface.pages.base_pages.quant.QuantUIObjects method) load_versions() (in module proteobench.io.params.quantms)

M

map_keys_to_desired_format() (in module proteobench.io.params.alphadia) match_brackets() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) max_peptide_length (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] mean_abs_epsilon (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] median_abs_epsilon (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] meta_data (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) meta_data_file (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute) meta_data_text (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) meta_file_uploader_uuid (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) min_peptide_length (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] module proteobench proteobench.datapoint proteobench.datapoint.quant_datapoint proteobench.exceptions proteobench.github proteobench.github.gh proteobench.io proteobench.io.params proteobench.io.params.alphadia proteobench.io.params.alphapept proteobench.io.params.diann proteobench.io.params.fragger proteobench.io.params.i2masschroq proteobench.io.params.maxquant proteobench.io.params.msaid proteobench.io.params.msangel proteobench.io.params.peaks 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_ion proteobench.io.parsing.parse_peptidoform proteobench.io.parsing.parse_settings proteobench.io.parsing.utils proteobench.modules proteobench.modules.constants proteobench.modules.quant 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_singlecell 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_quant proteobench.score proteobench.score.quant proteobench.score.quant.quantscores proteobench.utils proteobench.utils.submission webinterface webinterface.Home webinterface.pages 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.8_Quant_LFQ_DDA_ion_Astral webinterface.pages.base_pages webinterface.pages.base_pages.quant webinterface.pages.future_pages webinterface.pages.future_pages.6_Quant_LFQ_DIA_ion_singlecell webinterface.pages.markdown_files 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.pages_variables webinterface.pages.pages_variables.Quant 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_singlecell_variables webinterface.pages.texts webinterface.pages.texts.generic_texts webinterface.pages.texts.generic_texts_dia webinterface.pages.texts.proteobench_builder webinterface.streamlit_utils

module_id (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.DIAQuantIonModule 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_singlecell.DIAQuantIonModulediaSC attribute), [1] (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule attribute), [1] (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule attribute), [1]

N

name (proteobench.io.params.fragger.Parameter attribute) no_results (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute)

nr_prec (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1]

O

obtain_all_data_points() (proteobench.modules.quant.quant_base_module.QuantModule method)

P

Parameter (class in proteobench.io.params.fragger) parameters_additional (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) params_file_dict (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) params_json_dict (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) parse_button (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute) parse_cmdline_string() (in module proteobench.io.params.diann) parse_key_value() (in module proteobench.io.params.alphadia) 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_quantification_strategy() (in module proteobench.io.params.diann) parse_setting() (in module proteobench.io.params.diann) parse_settings_dir (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) ParseError ParseModificationSettings (class in proteobench.io.parsing.parse_settings) ParseSettingsBuilder (class in proteobench.io.parsing.parse_settings) ParseSettingsError ParseSettingsQuant (class in proteobench.io.parsing.parse_settings) placeholder_dataset_selection_container (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) placeholder_downloads_container (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) placeholder_fig_compare (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) placeholder_slider (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) placeholder_slider_submitted (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) placeholder_table (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) placeholder_table_submitted (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) plot_CV_violinplot() (proteobench.plotting.plot_quant.PlotDataPoint static method) plot_fold_change_histogram() (proteobench.plotting.plot_quant.PlotDataPoint static method) plot_ma_plot() (proteobench.plotting.plot_quant.PlotDataPoint static method) plot_metric() (proteobench.plotting.plot_quant.PlotDataPoint static method) PlotDataPoint (class in proteobench.plotting.plot_quant) PlotError precursor_column_name (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.DIAQuantIonModule 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_peptidoform_DDA.DDAQuantPeptidoformModule attribute) (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule attribute) precursor_mass_tolerance (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] precursor_name (proteobench.modules.quant.quant_lfq_ion_DIA_singlecell.DIAQuantIonModulediaSC attribute) prefix_params (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)

privacy_notice (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) 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_submission_form() (webinterface.pages.base_pages.quant.QuantUIObjects method) proteobench module proteobench.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.alphadia module proteobench.io.params.alphapept module proteobench.io.params.diann module proteobench.io.params.fragger module proteobench.io.params.i2masschroq module proteobench.io.params.maxquant module proteobench.io.params.msaid module proteobench.io.params.msangel module proteobench.io.params.peaks 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_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.quant 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_singlecell 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_quant module proteobench.score module proteobench.score.quant module proteobench.score.quant.quantscores module proteobench.utils module proteobench.utils.submission module proteobench_page_config() (in module webinterface.pages.texts.proteobench_builder) proteobench_sidebar() (in module webinterface.pages.texts.proteobench_builder) proteobench_version (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] ProteobenchError ProteoBenchParameters (class in proteobench.io.params) pull_req (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute)

Q

QuantDatapoint (class in proteobench.datapoint.quant_datapoint) QuantificationError

QuantModule (class in proteobench.modules.quant.quant_base_module) QuantScores (class in proteobench.score.quant.quantscores) QuantUIObjects (class in webinterface.pages.base_pages.quant)

R

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_peaks_settings() (in module proteobench.io.params.peaks) 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) result_perf (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)

result_performance_submission (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) results (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] run_benchmarking_process() (webinterface.pages.base_pages.quant.QuantUIObjects method) run_instructions (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute)

S

save_dataframe() (in module webinterface.streamlit_utils) save_intermediate_submission_data() (webinterface.pages.base_pages.quant.QuantUIObjects method) search_engine (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] search_engine_version (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] selectbox_id_submitted_uuid (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) selectbox_id_uuid (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) set_highlight_column_in_submitted_data() (webinterface.pages.base_pages.quant.QuantUIObjects method) shallow_clone() (proteobench.github.gh.GithubProteobotRepo static method) show_submission_success_message() (webinterface.pages.base_pages.quant.QuantUIObjects method) slider_id_submitted_uuid (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) slider_id_uuid (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)

software_name (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] software_version (proteobench.datapoint.quant_datapoint.QuantDatapoint attribute), [1] species_dict() (proteobench.io.parsing.parse_settings.ParseSettingsQuant method) species_expected_ratio() (proteobench.io.parsing.parse_settings.ParseSettingsQuant method) StreamlitLogger (class in webinterface.streamlit_utils) StreamlitPageHome (class in webinterface.Home) StreamlitUI (class in webinterface.pages.2_Quant_LFQ_DDA_ion_QExactive) (class in webinterface.pages.3_Quant_LFQ_DIA_ion_AIF) (class in webinterface.pages.4_Quant_LFQ_DIA_ion_diaPASEF) (class in webinterface.pages.5_Quant_LFQ_DDA_peptidoform) (class in webinterface.pages.6_Quant_LFQ_DIA_ion_Astral) (class in webinterface.pages.8_Quant_LFQ_DDA_ion_Astral) (class in webinterface.pages.future_pages.6_Quant_LFQ_DIA_ion_singlecell) submission_processing_warning (webinterface.pages.texts.generic_texts.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_dia.WebpageTexts.ShortMessages attribute) submit (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) submit_to_repository() (webinterface.pages.base_pages.quant.QuantUIObjects method)

T

table_id_uuid (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) texts (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)

title (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.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) to_lowercase() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform)

U

update_parameters_submission_form() (webinterface.pages.base_pages.quant.QuantUIObjects method)

V

value (proteobench.io.params.fragger.Parameter attribute) 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)

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) VariablesDIAQuantSC (class in webinterface.pages.pages_variables.Quant.lfq_DIA_ion_singlecell_variables)

W

webinterface module webinterface.Home module webinterface.pages 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.8_Quant_LFQ_DDA_ion_Astral module webinterface.pages.base_pages module webinterface.pages.base_pages.quant module webinterface.pages.future_pages module webinterface.pages.future_pages.6_Quant_LFQ_DIA_ion_singlecell module webinterface.pages.markdown_files 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.pages_variables module webinterface.pages.pages_variables.Quant 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_singlecell_variables module webinterface.pages.texts module webinterface.pages.texts.generic_texts module webinterface.pages.texts.generic_texts_dia module webinterface.pages.texts.proteobench_builder module webinterface.streamlit_utils module WebpageTexts (class in webinterface.pages.texts.generic_texts) (class in webinterface.pages.texts.generic_texts_dia) WebpageTexts.Help (class in webinterface.pages.texts.generic_texts) (class in webinterface.pages.texts.generic_texts_dia) WebpageTexts.ShortMessages (class in webinterface.pages.texts.generic_texts) (class in webinterface.pages.texts.generic_texts_dia) write_intermediate_raw() (proteobench.modules.quant.quant_base_module.QuantModule method) write_json_local_development() (proteobench.modules.quant.quant_base_module.QuantModule method)