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  "Package": "HaDeX2",
  "Title": "Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass\nSpectrometry Data",
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  "Description": "Processing, analysis and visualization of Hydrogen\nDeuterium eXchange monitored by Mass Spectrometry experiments\n(HDX-MS). 'HaDeX2' introduces a new standardized and\nreproducible workflow for the analysis of the HDX-MS data,\nincluding uncertainty propagation, data aggregation and\nvisualization on 3D structure. Additionally, it covers data\nexploration, quality control and generation of\npublication-quality figures. All functionalities are also\navailable in the accompanying 'shiny' app.",
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  "_exports": [
    "add_stat_dependency",
    "calculate_aggregated_diff_uptake",
    "calculate_aggregated_test_results",
    "calculate_aggregated_uptake",
    "calculate_auc",
    "calculate_back_exchange",
    "calculate_confidence_limit_values",
    "calculate_diff_uptake",
    "calculate_exp_masses",
    "calculate_exp_masses_per_replicate",
    "calculate_kinetics",
    "calculate_MHP",
    "calculate_p_value",
    "calculate_peptide_kinetics",
    "calculate_state_uptake",
    "create_aggregated_diff_uptake_dataset",
    "create_aggregated_uptake_dataset",
    "create_control_dataset",
    "create_diff_uptake_dataset",
    "create_kinetic_dataset",
    "create_overlap_distribution_dataset",
    "create_p_diff_uptake_dataset",
    "create_p_diff_uptake_dataset_with_confidence",
    "create_quality_control_dataset",
    "create_replicate_dataset",
    "create_state_comparison_dataset",
    "create_state_uptake_dataset",
    "create_uptake_dataset",
    "get_n_replicates",
    "get_peptide_sequence",
    "get_protein_coverage",
    "get_protein_redundancy",
    "get_replicate_list_sd",
    "get_residue_positions",
    "get_structure_color",
    "HaDeX_GUI",
    "HaDeXify",
    "install_GUI",
    "plot_aggregated_differential_uptake",
    "plot_aggregated_uptake",
    "plot_aggregated_uptake_structure",
    "plot_amino_distribution",
    "plot_butterfly",
    "plot_chiclet",
    "plot_coverage",
    "plot_coverage_heatmap",
    "plot_differential",
    "plot_differential_butterfly",
    "plot_differential_chiclet",
    "plot_differential_uptake_curve",
    "plot_manhattan",
    "plot_overlap",
    "plot_overlap_distribution",
    "plot_peptide_charge_measurement",
    "plot_peptide_mass_measurement",
    "plot_position_frequency",
    "plot_quality_control",
    "plot_replicate_histogram",
    "plot_replicate_mass_uptake",
    "plot_state_comparison",
    "plot_uncertainty",
    "plot_uptake_curve",
    "plot_volcano",
    "prepare_hdxviewer_export",
    "read_hdx",
    "reconstruct_sequence",
    "show_aggregated_uptake_data",
    "show_coverage_heatmap_data",
    "show_diff_uptake_data",
    "show_diff_uptake_data_confidence",
    "show_overlap_data",
    "show_p_diff_uptake_data",
    "show_peptide_charge_measurement",
    "show_peptide_mass_measurement",
    "show_quality_control_data",
    "show_replicate_histogram_data",
    "show_summary_data",
    "show_uc_data",
    "show_uptake_data",
    "update_hdexaminer_file"
  ],
  "_datasets": [
    {
      "name": "alpha_dat",
      "title": "Elongation factor eEF1B subunit alpha",
      "object": "alpha_dat",
      "class": [
        "hdx_data",
        "data.table",
        "data.frame"
      ],
      "fields": [
        "Protein",
        "Start",
        "End",
        "Sequence",
        "Modification",
        "MaxUptake",
        "MHP",
        "State",
        "Exposure",
        "File",
        "z",
        "Inten",
        "Center"
      ],
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      "table": true,
      "tojson": true
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  "_help": [
    {
      "page": "HaDeX2-package",
      "title": "HaDeX2",
      "topics": [
        "HaDeX2-package",
        "HaDeX2"
      ]
    },
    {
      "page": "add_stat_dependency",
      "title": "Calculates confidence limits",
      "topics": [
        "add_stat_dependency"
      ]
    },
    {
      "page": "alpha_dat",
      "title": "Elongation factor eEF1B subunit alpha",
      "topics": [
        "alpha_dat"
      ]
    },
    {
      "page": "calculate_aggregated_diff_uptake",
      "title": "Calculates aggregated deuterium uptake difference for one time point",
      "topics": [
        "calculate_aggregated_diff_uptake"
      ]
    },
    {
      "page": "calculate_aggregated_test_results",
      "title": "Aggregate test result",
      "topics": [
        "calculate_aggregated_test_results"
      ]
    },
    {
      "page": "calculate_aggregated_uptake",
      "title": "Calculates aggregated deuterium uptake for one time point",
      "topics": [
        "calculate_aggregated_uptake"
      ]
    },
    {
      "page": "calculate_auc",
      "title": "Calculate Area Under the Curve",
      "topics": [
        "calculate_auc"
      ]
    },
    {
      "page": "calculate_back_exchange",
      "title": "Back exchange estimation",
      "topics": [
        "calculate_back_exchange"
      ]
    },
    {
      "page": "calculate_confidence_limit_values",
      "title": "Calculate the value of confidence limit",
      "topics": [
        "calculate_confidence_limit_values"
      ]
    },
    {
      "page": "calculate_diff_uptake",
      "title": "Calculate differential uptake",
      "topics": [
        "calculate_diff_uptake"
      ]
    },
    {
      "page": "calculate_exp_masses",
      "title": "Calculate measured mass, aggregated from the replicates of the experiment",
      "topics": [
        "calculate_exp_masses"
      ]
    },
    {
      "page": "calculate_exp_masses_per_replicate",
      "title": "Calculate measured mass for each replicate of the experiment",
      "topics": [
        "calculate_exp_masses_per_replicate"
      ]
    },
    {
      "page": "calculate_kinetics",
      "title": "Calculate kinetics data",
      "topics": [
        "calculate_kinetics"
      ]
    },
    {
      "page": "calculate_MHP",
      "title": "Calculate MHP of the peptide",
      "topics": [
        "calculate_MHP"
      ]
    },
    {
      "page": "calculate_p_value",
      "title": "Create p-value dataset",
      "topics": [
        "calculate_p_value"
      ]
    },
    {
      "page": "calculate_peptide_kinetics",
      "title": "Calculate kinetics dataset",
      "topics": [
        "calculate_peptide_kinetics"
      ]
    },
    {
      "page": "calculate_state_uptake",
      "title": "Calculate deuterium uptake",
      "topics": [
        "calculate_state_uptake"
      ]
    },
    {
      "page": "create_aggregated_diff_uptake_dataset",
      "title": "Calculates aggregated uptake difference for peptide pool",
      "topics": [
        "create_aggregated_diff_uptake_dataset"
      ]
    },
    {
      "page": "create_aggregated_uptake_dataset",
      "title": "Calculates the aggregated uptake for peptide pool",
      "topics": [
        "create_aggregated_uptake_dataset"
      ]
    },
    {
      "page": "create_control_dataset",
      "title": "Create dataset with control",
      "topics": [
        "create_control_dataset"
      ]
    },
    {
      "page": "create_diff_uptake_dataset",
      "title": "Generate differential dataset",
      "topics": [
        "create_diff_uptake_dataset"
      ]
    },
    {
      "page": "create_kinetic_dataset",
      "title": "Create kinetics dataset for a list of peptides and their states",
      "topics": [
        "create_kinetic_dataset"
      ]
    },
    {
      "page": "create_overlap_distribution_dataset",
      "title": "Show overlap distribution data",
      "topics": [
        "create_overlap_distribution_dataset"
      ]
    },
    {
      "page": "create_p_diff_uptake_dataset",
      "title": "Create differential uptake dataset with p-value",
      "topics": [
        "create_p_diff_uptake_dataset"
      ]
    },
    {
      "page": "create_p_diff_uptake_dataset_with_confidence",
      "title": "Create differential dataset with statistical validity",
      "topics": [
        "create_p_diff_uptake_dataset_with_confidence"
      ]
    },
    {
      "page": "create_quality_control_dataset",
      "title": "Experiment quality control",
      "topics": [
        "create_quality_control_dataset"
      ]
    },
    {
      "page": "create_replicate_dataset",
      "title": "Create replicates data",
      "topics": [
        "create_replicate_dataset"
      ]
    },
    {
      "page": "create_state_comparison_dataset",
      "title": "Creates comparison uptake dataset",
      "topics": [
        "create_state_comparison_dataset"
      ]
    },
    {
      "page": "create_state_uptake_dataset",
      "title": "Create uptake dataset for chosen state",
      "topics": [
        "create_state_uptake_dataset"
      ]
    },
    {
      "page": "create_uptake_dataset",
      "title": "Create uptake dataset for multiple states",
      "topics": [
        "create_uptake_dataset"
      ]
    },
    {
      "page": "get_n_replicates",
      "title": "Get number of replicates",
      "topics": [
        "get_n_replicates"
      ]
    },
    {
      "page": "get_peptide_sequence",
      "title": "Get peptide sequence based on the position",
      "topics": [
        "get_peptide_sequence"
      ]
    },
    {
      "page": "get_protein_coverage",
      "title": "Get protein coverage",
      "topics": [
        "get_protein_coverage"
      ]
    },
    {
      "page": "get_protein_redundancy",
      "title": "Get protein redundancy",
      "topics": [
        "get_protein_redundancy"
      ]
    },
    {
      "page": "get_replicate_list_sd",
      "title": "Get replicates sd",
      "topics": [
        "get_replicate_list_sd"
      ]
    },
    {
      "page": "get_residue_positions",
      "title": "Get residue positions",
      "topics": [
        "get_residue_positions"
      ]
    },
    {
      "page": "get_structure_color",
      "title": "Get color palette for 3D structure",
      "topics": [
        "get_structure_color"
      ]
    },
    {
      "page": "HaDeX_GUI",
      "title": "HaDeX Graphical User Interface",
      "topics": [
        "HaDeX_GUI"
      ]
    },
    {
      "page": "HaDeXify",
      "title": "HaDeX customized ggplot theme",
      "topics": [
        "HaDeXify"
      ]
    },
    {
      "page": "install_GUI",
      "title": "Installs GUI package from GitHub",
      "topics": [
        "install_GUI"
      ]
    },
    {
      "page": "is_GUI_installed",
      "title": "Checks if GUI package is installed",
      "topics": [
        "is_GUI_installed"
      ]
    },
    {
      "page": "plot_aggregated_differential_uptake",
      "title": "Plots aggregated uptake difference",
      "topics": [
        "plot_aggregated_differential_uptake"
      ]
    },
    {
      "page": "plot_aggregated_uptake",
      "title": "Plots aggregated uptake",
      "topics": [
        "plot_aggregated_uptake"
      ]
    },
    {
      "page": "plot_aggregated_uptake_structure",
      "title": "Plot aggregated uptake on the 3D structure",
      "topics": [
        "plot_aggregated_uptake_structure"
      ]
    },
    {
      "page": "plot_amino_distribution",
      "title": "generate_amino_distribution",
      "topics": [
        "plot_amino_distribution"
      ]
    },
    {
      "page": "plot_butterfly",
      "title": "Butterfly deuterium uptake plot",
      "topics": [
        "plot_butterfly"
      ]
    },
    {
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