Package index
-
-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