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All functions

-package HaDeX-package HaDeX
HaDeX
HaDeX_GUI()
HaDeX Graphical User Interface
HaDeXify()
HaDeX customized ggplot theme
add_stat_dependency()
Calculates confidence limits
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_structure_color()
Get color pallette 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