Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data
Calculates confidence limits
Calculates aggregated deuterium uptake difference for one time point
Aggregate test result
Calculates aggregated deuterium uptake for one time point
Calculate Area Under the Curve
Back exchange estimation
Calculate the value of confidence limit
Calculate differential uptake
Calculate measured mass for each replicate of the experiment
Calculate measured mass, aggregated from the replicates of the experim...
Calculate kinetics data
Calculate MHP of the peptide
Create p-value dataset
Calculate kinetics dataset
Calculate deuterium uptake
Calculates aggregated uptake difference for peptide pool
Calculates the aggregated uptake for peptide pool
Create dataset with control
Generate differential dataset
Create kinetics dataset for a list of peptides and their states
Show overlap distribution data
Create differential dataset with statistical validity
Create differential uptake dataset with p-value
Experiment quality control
Create replicates data
Creates comparison uptake dataset
Create uptake dataset for chosen state
Create uptake dataset for multiple states
Get number of replicates
Get peptide sequence based on the position
Get protein coverage
Get protein redundancy
Get replicates sd
Get residue positions
Get color palette for 3D structure
HaDeX Graphical User Interface
HaDeX2
HaDeX customized ggplot theme
Creation of validated hdx_data class
Installs GUI package from GitHub
Checks if GUI package is installed
Constructor of hdx_data class
Plots aggregated uptake difference
Plot aggregated uptake on the 3D structure
Plots aggregated uptake
generate_amino_distribution
Butterfly deuterium uptake plot
Chiclet deuterium uptake plot
Coverage heatmap
Peptide coverage
Butterfly differential deuterium uptake plot
Chiclet differential deuterium uptake plot
Plot differential uptake curve
Differential plot
Manhattan plot
Plot overlap distribution
Plot overlap data
Plot peptide charge measurement
Plot peptide mass measurement
Position frequency
Plot quality control data
Plot replicates histogram
Replicate mass uptake curve
State deuterium uptake comparison
Uncertainty of the peptide measurements
Deuterium uptake curve
Volcano plot
Prepares data export for HDX-Viewer
Read HDX-MS data file
Reconstruct protein sequence
Show aggregated values in friendly form
Coverage heatmap data
Differential uptake data with confidence
Differential deuterium uptake data
Show data on peptide overlap
Differential deuterium uptake data
Show peptide charge measurement
Show peptide mass measurement
Show quality control data
Show replicate data
Summary data
Deuterium uptake curve data
Deuterium uptake data
Update HDeXaminer datafile
Validator on hdx_data class
Processing, analysis and visualization of Hydrogen Deuterium eXchange monitored by Mass Spectrometry experiments (HDX-MS). 'HaDeX2' introduces a new standardized and reproducible workflow for the analysis of the HDX-MS data, including uncertainty propagation, data aggregation and visualization on 3D structure. Additionally, it covers data exploration, quality control and generation of publication-quality figures. All functionalities are also available in the accompanying 'shiny' app.