ProteoGyver documentation

Welcome to the ProteoGyver documentation!

This documentation includes:

• User guide and installation instructions

• API reference for all modules

• Code examples and usage patterns

Contents:

• Proteogyver
  • Table of contents:
  • Security and compatibility
  • Example use cases
  • QC and quick analysis toolset
    • Core Analysis Workflows
    • Usage
    • Input size and scale
    • Input Data Format
      • Limitations
    • Input options guide
      • General Input Options (Main Sidebar)
      • Proteomics Workflow Options
      • Interactomics Workflow Options
      • SAINT Filtering Options (Post-SAINT Analysis)
    • Algorithm details
    • PTM workflow
    • Pipeline mode for automated processing
      • Pipeline input toml
      • Parameters not in the input toml
      • Initiating pipeline analysis via API
      • Autocleaning of pipeline module inputs
  • Additional Tools
    • MS Inspector
      • Features
      • Usage
      • Notes
    • Microscopy Image Colocalizer
  • Installation
    • MS run data pre-analysis
    • Docker Installation (recommended)
      • Running the docker images
        • Changing parameters
      • Run the container
        • Volume paths
  • Creating and updating the database
    • Update running order:
      • Forcing an update
    • Adding MS run data
    • Adding new crapome or control sets:
    • Adding other new tables:
    • Deleting data
    • Update logging
  • Building the docker images:
    • Build the Docker images and run the PG updater
      • Prerequisites:
      • Used external data
      • Build the main docker image.
  • Rare use cases
    • Embedding other websites as tabs within Proteogyver
    • Adding custom tools as tabs to Proteogyver
    • Accessing the database from other tools
  • How to cite
• Example Proteomics usecase for ProteoGyver
  • Software and data utilized
  • Proteogyver
  • Data upload
• Example Interactomcis usecase for ProteoGyver
  • Software and data prerequisites
  • Proteogyver
  • Data upload
• ProteoGyver User Guide
  • QC and data analysis
    • Data upload
      • Sample table
        • Example Proteomics sample table
        • Example Interactomics sample table
      • Data table
    • Running ProteoGyver
      • QC results
      • Workflow specific figures
      • Workflow-specific input
        • Proteomics
          • Missing value slider
          • Example with 60 % filter (default):
          • Imputation choice
          • Normalization choice
          • Comparisons
          • Thresholds
        • Interactomics
          • Initial input
          • Post-SAINTexpress input
  • MS Analytics dashboard
  • Colocalizer
• Code Reference
  • app package
    • Subpackages
      • app.components package
        • Subpackages
          • app.components.api_tools package
          • app.components.enrichment package
          • app.components.figures package
          • app.components.tools package
        • Submodules
        • app.components.EnrichmentAdmin module
          • EnrichmentAdmin
        • app.components.MS_run_json_parser module
        • app.components.cleanup_tasks module
        • app.components.db_functions module
          • add_column()
          • add_multiple_records()
          • add_record()
          • create_connection()
          • delete_multiple_records()
          • delete_record()
          • drop_table()
          • dump_full_database_to_csv()
          • export_snapshot()
          • generate_database_table_templates_as_tsvs()
          • get_contaminants()
          • get_database_versions()
          • get_from_table()
          • get_from_table_by_list_criteria()
          • get_from_table_match_with_priority()
          • get_full_table_as_pd()
          • get_last_update()
          • get_table_column_names()
          • is_test_db()
          • list_tables()
          • map_protein_info()
          • modify_multiple_records()
          • modify_record()
          • remove_column()
          • rename_column()
        • app.components.figure_functions module
          • improve_text_position()
        • app.components.file_upload_api module
          • register_file_upload_api()
        • app.components.infra module
          • Functions
          • Constants
        • app.components.interactomics module
          • logger
          • add_bait_column()
          • add_crapome()
          • count_knowns()
          • create_dummy_list_txt()
          • do_ms_microscopy()
          • do_network()
          • enrich()
          • filter_controls_by_similarity()
          • generate_saint_container()
          • get_saint_matrix()
          • known_plot()
          • make_saint_dict()
          • map_intensity()
          • network_display_data()
          • pca()
          • prepare_controls()
          • prepare_crapome()
          • run_saint()
          • saint_cmd()
          • saint_counts()
          • saint_filtering()
          • saint_histogram()
        • app.components.mathparser module
          • MathParser
        • app.components.matrix_functions module
          • compute_zscore()
          • compute_zscore_based_deviation_from_control()
          • count_per_sample()
          • do_pca()
          • filter_missing()
          • hierarchical_clustering()
          • impute()
          • impute_gaussian()
          • impute_minprob()
          • impute_minprob_df()
          • impute_minval()
          • median_normalize()
          • normalize()
          • quantile_normalize()
          • ranked_dist()
          • ranked_dist_n_per_run()
          • reverse_log2()
        • app.components.ms_microscopy module
          • draw_localization_heatmap()
          • draw_localization_plot()
          • generate_msmic_dataframes()
          • localization_graph()
          • tweak_fig_size_hw()
        • app.components.parsing module
          • check_bait()
          • check_comparison_file()
          • check_numeric()
          • check_required_columns()
          • check_sample_table_column()
          • clean_column_name()
          • clean_sample_names()
          • delete_samples()
          • format_data()
          • format_sample_group_name()
          • generate_replicate_name()
          • get_distribution_title()
          • guess_controls()
          • handle_mztab()
          • identify_columns()
          • parse_comparisons()
          • parse_data_file()
          • parse_parameters()
          • parse_sample_table()
          • read_data_from_content()
          • read_df_from_content()
          • read_dia_nn()
          • read_fragpipe()
          • read_matrix()
          • remove_all_na()
          • remove_duplicate_protein_groups()
          • remove_file_path()
          • remove_filepath_from_columns()
          • remove_from_table()
          • remove_rawfile_ending()
          • rename_columns_and_update_expdesign()
          • sdrf_to_table()
          • unmix_dtypes()
          • update_nested_dict()
          • validate_basic_inputs()
        • app.components.proteomics module
          • clustermap()
          • differential_abundance()
          • imputation()
          • missing_values_in_other_samples()
          • na_filter()
          • normalization()
          • pca()
          • perc_cvplot()
        • app.components.qc_analysis module
          • common_proteins()
          • commonality_plot()
          • count_plot()
          • coverage_plot()
          • distribution_plot()
          • generate_commonality_container()
          • mean_plot()
          • missing_plot()
          • parse_tic_data()
          • reproducibility_plot()
          • sum_plot()
        • app.components.quick_stats module
          • anova()
          • differential()
          • get_common_data()
          • get_comparative_data()
          • get_count_data()
          • get_coverage_data()
          • get_mean_data()
          • get_na_data()
          • get_sum_data()
        • app.components.text_handling module
          • clean_text()
          • remove_accent_characters()
          • replace_accent_and_special_characters()
          • replace_special_characters()
          • sanitize_for_database_use()
        • app.components.tooltips module
          • generic_tooltip()
          • interactomics_select_top_controls_tooltip()
          • na_tooltip()
          • nearest_tooltip()
          • rescue_tooltip()
          • test_type_tooltip()
        • app.components.ui_components module
          • HEADER_DICT
          • checklist()
          • discard_samples_checklist()
          • interactomics_area()
          • interactomics_control_col()
          • interactomics_crapome_col()
          • interactomics_enrichment_col()
          • interactomics_inbuilt_control_col()
          • interactomics_input_card()
          • main_content_div()
          • main_sidebar()
          • make_du_uploader()
          • modals()
          • navbar()
          • post_saint_container()
          • proteomics_area()
          • proteomics_input_card()
          • qc_area()
          • range_input()
          • saint_filtering_container()
          • table_of_contents()
          • upload_area()
          • workflow_area()
        • Module contents
      • app.pages package
        • Submodules
        • app.pages.Colocalizer module
        • app.pages.Documentation module
        • app.pages.MS_Inspector module
        • app.pages.QC_and_data_analysis module
        • Module contents
      • app.pipeline_module package
        • Submodules
        • app.pipeline_module.batch_data_store_builder module
          • build_data_stores_from_batch_output()
          • build_interactomics_data_stores()
          • build_proteomics_data_stores()
          • build_qc_data_stores()
          • build_replicate_colors_stores()
          • build_upload_data_store()
          • create_data_store_component()
          • save_batch_data_using_infra()
        • app.pipeline_module.batch_figure_builder_from_divs module
          • build_analysis_divs_from_saved_divs()
          • get_commonality_pdf_data()
          • load_div_pickle()
          • main()
          • save_batch_figures_using_saved_divs()
        • app.pipeline_module.pipeline_batch module
          • BatchConfig
          • dash_to_wire()
          • run_pipeline()
        • app.pipeline_module.pipeline_from_toml module
          • load_config()
          • load_pipeline_parameters()
        • app.pipeline_module.pipeline_input_watcher module
        • Module contents
      • app.resources package
        • Submodules
        • app.resources.get_cpu_count module
        • Module contents
    • Submodules
    • app.app module
      • celery_app
      • app
      • server
      • logger
      • create_navbar()
      • main()
      • toggle_navbar_collapse()
    • app.database_admin module
      • clean_database()
      • create_sqlite_from_schema()
      • get_external_versions()
      • last_update()
      • main()
    • app.database_updater module
      • get_dataframe_differences()
      • handle_merg_chunk()
      • handle_mods()
      • handle_new()
      • merge_multiple_string_dataframes()
      • stream_flattened_rows()
      • update_database()
      • update_external_data()
      • update_knowns()
      • update_log_table()
      • update_table_with_file()
      • update_uniprot()
      • update_version_table()
    • app.element_styles module
    • app.embedded_page_updater module
      • create_page_file()
      • parse_embed_file()
      • update_pages()
    • app.run_as_pipeline module
      • main()
      • run_batch_pipeline()
    • Module contents
  • MSParser Package
    • Submodules
    • MSParser.ms_name_identifier module
      • identify()
    • MSParser.MSparser module
      • analyze()
      • calculate_auc()
      • count_intercepts()
      • handle_data()
      • main()
      • parse_d()
      • parse_raw()
      • read_toml()
      • remove_accent_characters()
      • remove_rawfile_ending()
      • replace_special_characters()
    • MSParser.parse_thermo module
      • deduplicate_nested_dicts()
      • get_scantypes()
      • get_traces()
      • parse_file()
      • roundup()
    • MSParser.parse_timstof module
      • get_directory_size()
      • get_traces()
      • parse_file()
    • Module contents

Indices and tables

• Index

• Module Index

• Search Page