HaDeX2-package          HaDeX2
HaDeX_GUI               HaDeX Graphical User Interface
HaDeXify                HaDeX customized ggplot theme
add_stat_dependency     Calculates confidence limits
alpha_dat               Elongation factor eEF1B subunit alpha
calculate_MHP           Calculate MHP of the peptide
calculate_aggregated_diff_uptake
                        Calculates aggregated deuterium uptake
                        difference for one time point
calculate_aggregated_test_results
                        Aggregate test result
calculate_aggregated_uptake
                        Calculates aggregated deuterium uptake for one
                        time point
calculate_auc           Calculate Area Under the Curve
calculate_back_exchange
                        Back exchange estimation
calculate_confidence_limit_values
                        Calculate the value of confidence limit
calculate_diff_uptake   Calculate differential uptake
calculate_exp_masses    Calculate measured mass, aggregated from the
                        replicates of the experiment
calculate_exp_masses_per_replicate
                        Calculate measured mass for each replicate of
                        the experiment
calculate_kinetics      Calculate kinetics data
calculate_p_value       Create p-value dataset
calculate_peptide_kinetics
                        Calculate kinetics dataset
calculate_state_uptake
                        Calculate deuterium uptake
create_aggregated_diff_uptake_dataset
                        Calculates aggregated uptake difference for
                        peptide pool
create_aggregated_uptake_dataset
                        Calculates the aggregated uptake for peptide
                        pool
create_control_dataset
                        Create dataset with control
create_diff_uptake_dataset
                        Generate differential dataset
create_kinetic_dataset
                        Create kinetics dataset for a list of peptides
                        and their states
create_overlap_distribution_dataset
                        Show overlap distribution data
create_p_diff_uptake_dataset
                        Create differential uptake dataset with p-value
create_p_diff_uptake_dataset_with_confidence
                        Create differential dataset with statistical
                        validity
create_quality_control_dataset
                        Experiment quality control
create_replicate_dataset
                        Create replicates data
create_state_comparison_dataset
                        Creates comparison uptake dataset
create_state_uptake_dataset
                        Create uptake dataset for chosen state
create_uptake_dataset   Create uptake dataset for multiple states
get_n_replicates        Get number of replicates
get_peptide_sequence    Get peptide sequence based on the position
get_protein_coverage    Get protein coverage
get_protein_redundancy
                        Get protein redundancy
get_replicate_list_sd   Get replicates sd
get_residue_positions   Get residue positions
get_structure_color     Get color palette for 3D structure
install_GUI             Installs GUI package from GitHub
is_GUI_installed        Checks if GUI package is installed
plot_aggregated_differential_uptake
                        Plots aggregated uptake difference
plot_aggregated_uptake
                        Plots aggregated uptake
plot_aggregated_uptake_structure
                        Plot aggregated uptake on the 3D structure
plot_amino_distribution
                        generate_amino_distribution
plot_butterfly          Butterfly deuterium uptake plot
plot_chiclet            Chiclet deuterium uptake plot
plot_coverage           Peptide coverage
plot_coverage_heatmap   Coverage heatmap
plot_differential       Differential plot
plot_differential_butterfly
                        Butterfly differential deuterium uptake plot
plot_differential_chiclet
                        Chiclet differential deuterium uptake plot
plot_differential_uptake_curve
                        Plot differential uptake curve
plot_manhattan          Manhattan plot
plot_overlap            Plot overlap data
plot_overlap_distribution
                        Plot overlap distribution
plot_peptide_charge_measurement
                        Plot peptide charge measurement
plot_peptide_mass_measurement
                        Plot peptide mass measurement
plot_position_frequency
                        Position frequency
plot_quality_control    Plot quality control data
plot_replicate_histogram
                        Plot replicates histogram
plot_replicate_mass_uptake
                        Replicate mass uptake curve
plot_state_comparison   State deuterium uptake comparison
plot_uncertainty        Uncertainty of the peptide measurements
plot_uptake_curve       Deuterium uptake curve
plot_volcano            Volcano plot
prepare_hdxviewer_export
                        Prepares data export for HDX-Viewer
read_hdx                Read HDX-MS data file
reconstruct_sequence    Reconstruct protein sequence
show_aggregated_uptake_data
                        Show aggregated values in friendly form
show_coverage_heatmap_data
                        Coverage heatmap data
show_diff_uptake_data   Differential deuterium uptake data
show_diff_uptake_data_confidence
                        Differential uptake data with confidence
show_overlap_data       Show data on peptide overlap
show_p_diff_uptake_data
                        Differential deuterium uptake data
show_peptide_charge_measurement
                        Show peptide charge measurement
show_peptide_mass_measurement
                        Show peptide mass measurement
show_quality_control_data
                        Show quality control data
show_replicate_histogram_data
                        Show replicate data
show_summary_data       Summary data
show_uc_data            Deuterium uptake curve data
show_uptake_data        Deuterium uptake data
update_hdexaminer_file
                        Update HDeXaminer datafile
