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  "Title": "Bottom-Up Proteomics and LiP-MS Quality Control and Data\nAnalysis Tools",
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    "assign_missingness",
    "assign_peptide_type",
    "barcode_plot",
    "calculate_aa_scores",
    "calculate_diff_abundance",
    "calculate_go_enrichment",
    "calculate_kegg_enrichment",
    "calculate_protein_abundance",
    "calculate_sequence_coverage",
    "calculate_treatment_enrichment",
    "correct_lip_for_abundance",
    "create_queue",
    "create_structure_contact_map",
    "create_synthetic_data",
    "diff_abundance",
    "drc_4p_plot",
    "extract_metal_binders",
    "fetch_alphafold_aligned_error",
    "fetch_alphafold_prediction",
    "fetch_chebi",
    "fetch_eco",
    "fetch_go",
    "fetch_interpro",
    "fetch_kegg",
    "fetch_metal_pdb",
    "fetch_mobidb",
    "fetch_pdb",
    "fetch_pdb_structure",
    "fetch_quickgo",
    "fetch_uniprot",
    "fetch_uniprot_proteome",
    "filter_cv",
    "find_peptide",
    "find_peptide_in_structure",
    "fit_drc_4p",
    "go_enrichment",
    "impute",
    "impute_randomforest",
    "kegg_enrichment",
    "map_peptides_on_structure",
    "median_normalisation",
    "network_analysis",
    "normalise",
    "parallel_create_structure_contact_map",
    "parallel_fit_drc_4p",
    "peptide_profile_plot",
    "peptide_type",
    "plot_drc_4p",
    "plot_peptide_profiles",
    "plot_pval_distribution",
    "predict_alphafold_domain",
    "pval_distribution_plot",
    "qc_charge_states",
    "qc_contaminants",
    "qc_cvs",
    "qc_data_completeness",
    "qc_ids",
    "qc_intensity_distribution",
    "qc_median_intensities",
    "qc_missed_cleavages",
    "qc_pca",
    "qc_peak_width",
    "qc_peptide_type",
    "qc_proteome_coverage",
    "qc_ranked_intensities",
    "qc_sample_correlation",
    "qc_sequence_coverage",
    "randomise_queue",
    "read_protti",
    "scale_protti",
    "sequence_coverage",
    "treatment_enrichment",
    "ttest_protti",
    "volcano_plot",
    "volcano_protti",
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      "fields": [],
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      "title": "Analyse protein interaction network for significant hits",
      "topics": [
        "analyse_functional_network"
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    {
      "page": "anova_protti",
      "title": "Perform ANOVA",
      "topics": [
        "anova_protti"
      ]
    },
    {
      "page": "assign_missingness",
      "title": "Assignment of missingness types",
      "topics": [
        "assign_missingness"
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    },
    {
      "page": "assign_peptide_type",
      "title": "Assign peptide type",
      "topics": [
        "assign_peptide_type"
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    },
    {
      "page": "barcode_plot",
      "title": "Barcode plot",
      "topics": [
        "barcode_plot"
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    },
    {
      "page": "calculate_aa_scores",
      "title": "Calculate scores for each amino acid position in a protein sequence",
      "topics": [
        "calculate_aa_scores"
      ]
    },
    {
      "page": "calculate_diff_abundance",
      "title": "Calculate differential abundance between conditions",
      "topics": [
        "calculate_diff_abundance"
      ]
    },
    {
      "page": "calculate_go_enrichment",
      "title": "Perform gene ontology enrichment analysis",
      "topics": [
        "calculate_go_enrichment"
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    },
    {
      "page": "calculate_imputation",
      "title": "Sampling of values for imputation",
      "topics": [
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    },
    {
      "page": "calculate_kegg_enrichment",
      "title": "Perform KEGG pathway enrichment analysis",
      "topics": [
        "calculate_kegg_enrichment"
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    },
    {
      "page": "calculate_protein_abundance",
      "title": "Label-free protein quantification",
      "topics": [
        "calculate_protein_abundance"
      ]
    },
    {
      "page": "calculate_sequence_coverage",
      "title": "Protein sequence coverage",
      "topics": [
        "calculate_sequence_coverage"
      ]
    },
    {
      "page": "calculate_treatment_enrichment",
      "title": "Check treatment enrichment",
      "topics": [
        "calculate_treatment_enrichment"
      ]
    },
    {
      "page": "correct_lip_for_abundance",
      "title": "Protein abundance correction for LiP-data",
      "topics": [
        "correct_lip_for_abundance"
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    },
    {
      "page": "create_queue",
      "title": "Creates a mass spectrometer queue for Xcalibur",
      "topics": [
        "create_queue"
      ]
    },
    {
      "page": "create_structure_contact_map",
      "title": "Creates a contact map of all atoms from a structure file",
      "topics": [
        "create_structure_contact_map"
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    },
    {
      "page": "create_synthetic_data",
      "title": "Creates a synthetic limited proteolysis proteomics dataset",
      "topics": [
        "create_synthetic_data"
      ]
    },
    {
      "page": "drc_4p",
      "title": "Dose response curve helper function",
      "topics": [
        "drc_4p"
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    },
    {
      "page": "drc_4p_plot",
      "title": "Plotting of four-parameter dose response curves",
      "topics": [
        "drc_4p_plot"
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    },
    {
      "page": "extract_metal_binders",
      "title": "Extract metal-binding protein information from UniProt",
      "topics": [
        "extract_metal_binders"
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    },
    {
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