Man pages for HaDeX2
Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data
| add_stat_dependency | Calculates confidence limits |
| alpha_dat | Elongation factor eEF1B subunit alpha |
| calculate_aggregated_diff_uptake | Calculates aggregated deuterium uptake difference for one... |
| 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... |
| calculate_exp_masses_per_replicate | Calculate measured mass for each replicate of the experiment |
| calculate_kinetics | Calculate kinetics data |
| calculate_MHP | Calculate MHP of the peptide |
| calculate_peptide_kinetics | Calculate kinetics dataset |
| calculate_p_value | Create p-value 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... |
| 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 |
| HaDeX2-package | HaDeX2 |
| HaDeX_GUI | HaDeX Graphical User Interface |
| HaDeXify | HaDeX customized ggplot theme |
| hdx_data | Creation of validated hdx_data class |
| install_GUI | Installs GUI package from GitHub |
| is_GUI_installed | Checks if GUI package is installed |
| new_hdx_data | Constructor of hdx_data class |
| 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 |
| validate_hdx_data | Validator on hdx_data class |
