Package: HaDeX2 1.0.0

Weronika Puchala

HaDeX2: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

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.

Authors:Weronika Puchala [cre, aut], Michal Burdukiewicz [aut], Dominik Rafacz [ctb], Krystyna Grzesiak [ctb]

HaDeX2_1.0.0.tar.gz
HaDeX2_1.0.0.zip(r-4.7)HaDeX2_1.0.0.zip(r-4.6)HaDeX2_1.0.0.zip(r-4.5)
HaDeX2_1.0.0.tgz(r-4.6-any)HaDeX2_1.0.0.tgz(r-4.5-any)
HaDeX2_1.0.0.tar.gz(r-4.7-any)HaDeX2_1.0.0.tar.gz(r-4.6-any)
HaDeX2_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HaDeX2/json (API)

# Install 'HaDeX2' in R:
install.packages('HaDeX2', repos = c('https://hadexversum.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hadexversum/hadex2/issues

Pkgdown/docs site:https://hadexversum.github.io

Datasets:
  • alpha_dat - Elongation factor eEF1B subunit alpha

On CRAN:

Conda:

hdx-msmass-spectrometry

7.01 score 2 stars 13 scripts 176 downloads 80 exports 81 dependencies

Last updated from:41769f6088. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK265
source / vignettesOK257
linux-release-x86_64OK264
macos-release-arm64OK306
macos-oldrel-arm64OK252
windows-develOK152
windows-releaseOK264
windows-oldrelOK208
wasm-releaseOK142

Exports:add_stat_dependencycalculate_aggregated_diff_uptakecalculate_aggregated_test_resultscalculate_aggregated_uptakecalculate_auccalculate_back_exchangecalculate_confidence_limit_valuescalculate_diff_uptakecalculate_exp_massescalculate_exp_masses_per_replicatecalculate_kineticscalculate_MHPcalculate_p_valuecalculate_peptide_kineticscalculate_state_uptakecreate_aggregated_diff_uptake_datasetcreate_aggregated_uptake_datasetcreate_control_datasetcreate_diff_uptake_datasetcreate_kinetic_datasetcreate_overlap_distribution_datasetcreate_p_diff_uptake_datasetcreate_p_diff_uptake_dataset_with_confidencecreate_quality_control_datasetcreate_replicate_datasetcreate_state_comparison_datasetcreate_state_uptake_datasetcreate_uptake_datasetget_n_replicatesget_peptide_sequenceget_protein_coverageget_protein_redundancyget_replicate_list_sdget_residue_positionsget_structure_colorHaDeX_GUIHaDeXifyinstall_GUIplot_aggregated_differential_uptakeplot_aggregated_uptakeplot_aggregated_uptake_structureplot_amino_distributionplot_butterflyplot_chicletplot_coverageplot_coverage_heatmapplot_differentialplot_differential_butterflyplot_differential_chicletplot_differential_uptake_curveplot_manhattanplot_overlapplot_overlap_distributionplot_peptide_charge_measurementplot_peptide_mass_measurementplot_position_frequencyplot_quality_controlplot_replicate_histogramplot_replicate_mass_uptakeplot_state_comparisonplot_uncertaintyplot_uptake_curveplot_volcanoprepare_hdxviewer_exportread_hdxreconstruct_sequenceshow_aggregated_uptake_datashow_coverage_heatmap_datashow_diff_uptake_datashow_diff_uptake_data_confidenceshow_overlap_datashow_p_diff_uptake_datashow_peptide_charge_measurementshow_peptide_mass_measurementshow_quality_control_datashow_replicate_histogram_datashow_summary_datashow_uc_datashow_uptake_dataupdate_hdexaminer_file

Dependencies:backportsbase64encbio3dbitbit64bslibcachemcellrangercheckmateclicliprcpp11crayoncurldata.tabledigestdplyrevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggiraphggplot2gluegridExtragtablehighrhmshtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglifecyclemagickmagrittrMASSmemoisemimepillarpkgconfigprettyunitsprogresspurrrr3dmolR6rappdirsRColorBrewerRcppreadrreadxlrematchremotesrlangrmarkdownS7sassscalesstringistringrsystemfontstibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunyaml

Calculations
Initial processing of the data | Calculation of the deuterium uptake | Deuterium uptake | Fractional deuterium uptake | Theoretical deuterium uptake | Theoretical fractional deuterium uptake | Differential values | Deuterium uptake averaging | Back-exchange | AUC
Rendered fromdatafiles.Rmdusingknitr::rmarkdown

Last update: 2026-02-08
Started: 2020-08-31

Data visualization
Visualizing HDX-MS data | Comparison plot | Woods plot | Butterfly plot | Butterfly differential plot | Chiclet plot | Chiclet differential plot | Volcano plot | Uptake curve | Uncertainty plot | Manhattan plot | High-resolution plot | Differential High-resolution plot | High-resolution on 3D structure | Coverage heatmap | Summary of the uptake plots
Rendered fromvisualization.Rmdusingknitr::rmarkdown

Last update: 2026-02-08
Started: 2021-04-15

Importing data
DynamX cluster file | DynamX state file | HDeXaminer
Rendered fromdata_input.Rmdusingknitr::rmarkdown

Last update: 2026-02-08
Started: 2025-03-12

Quality control
Replicates | Uncertainty | Measurement variability plot | Back-exchange
Rendered fromquality_control.Rmdusingknitr::rmarkdown

Last update: 2026-02-08
Started: 2025-03-12

Statistics
Uncertainty propagation | Hybrid testing | Houde interval | Student's t-test
Rendered fromstatistics.Rmdusingknitr::rmarkdown

Last update: 2026-02-08
Started: 2025-12-02

Mass calculation
Comparison of results with weighted mean and without
Rendered frommass_comparison.Rmdusingknitr::rmarkdown

Last update: 2026-02-05
Started: 2025-02-26

Code usage
Convention | Example of use | Read data file | Different forms of visualization
Rendered fromusage.Rmdusingknitr::rmarkdown

Last update: 2026-02-01
Started: 2021-06-01

Comparison between versions
Comparison of visualization types | New web-server features | Functionality mapping between HaDeX and HaDeX2 | Performance benchmarking of HaDeX and HaDeX2 | HaDeX2 design
Rendered fromversion_comparison.Rmdusingknitr::rmarkdown

Last update: 2026-02-01
Started: 2025-11-18

Data aggregation
Aggregation of the data - visualization
Rendered fromtransformation.Rmdusingknitr::rmarkdown

Last update: 2026-02-01
Started: 2025-02-26

Glossary
Variables | Time points of measurement | Deuterium uptake values | Experimental conditions
Rendered fromglossary.Rmdusingknitr::rmarkdown

Last update: 2026-02-01
Started: 2020-08-31

Example HDX-MS data analysis
Introduction | Data analysis with HaDeX2 | Input Data | Deuterium uptake | Time-based data | Hi-res + 3D | Measurements | Sequence data | Summary
Rendered fromexample.Rmdusingknitr::rmarkdown

Last update: 2026-01-14
Started: 2025-08-14

Readme and manuals

Help Manual

Help pageTopics
HaDeX2HaDeX2-package HaDeX2
Calculates confidence limitsadd_stat_dependency
Elongation factor eEF1B subunit alphaalpha_dat
Calculates aggregated deuterium uptake difference for one time pointcalculate_aggregated_diff_uptake
Aggregate test resultcalculate_aggregated_test_results
Calculates aggregated deuterium uptake for one time pointcalculate_aggregated_uptake
Calculate Area Under the Curvecalculate_auc
Back exchange estimationcalculate_back_exchange
Calculate the value of confidence limitcalculate_confidence_limit_values
Calculate differential uptakecalculate_diff_uptake
Calculate measured mass, aggregated from the replicates of the experimentcalculate_exp_masses
Calculate measured mass for each replicate of the experimentcalculate_exp_masses_per_replicate
Calculate kinetics datacalculate_kinetics
Calculate MHP of the peptidecalculate_MHP
Create p-value datasetcalculate_p_value
Calculate kinetics datasetcalculate_peptide_kinetics
Calculate deuterium uptakecalculate_state_uptake
Calculates aggregated uptake difference for peptide poolcreate_aggregated_diff_uptake_dataset
Calculates the aggregated uptake for peptide poolcreate_aggregated_uptake_dataset
Create dataset with controlcreate_control_dataset
Generate differential datasetcreate_diff_uptake_dataset
Create kinetics dataset for a list of peptides and their statescreate_kinetic_dataset
Show overlap distribution datacreate_overlap_distribution_dataset
Create differential uptake dataset with p-valuecreate_p_diff_uptake_dataset
Create differential dataset with statistical validitycreate_p_diff_uptake_dataset_with_confidence
Experiment quality controlcreate_quality_control_dataset
Create replicates datacreate_replicate_dataset
Creates comparison uptake datasetcreate_state_comparison_dataset
Create uptake dataset for chosen statecreate_state_uptake_dataset
Create uptake dataset for multiple statescreate_uptake_dataset
Get number of replicatesget_n_replicates
Get peptide sequence based on the positionget_peptide_sequence
Get protein coverageget_protein_coverage
Get protein redundancyget_protein_redundancy
Get replicates sdget_replicate_list_sd
Get residue positionsget_residue_positions
Get color palette for 3D structureget_structure_color
HaDeX Graphical User InterfaceHaDeX_GUI
HaDeX customized ggplot themeHaDeXify
Installs GUI package from GitHubinstall_GUI
Checks if GUI package is installedis_GUI_installed
Plots aggregated uptake differenceplot_aggregated_differential_uptake
Plots aggregated uptakeplot_aggregated_uptake
Plot aggregated uptake on the 3D structureplot_aggregated_uptake_structure
generate_amino_distributionplot_amino_distribution
Butterfly deuterium uptake plotplot_butterfly
Chiclet deuterium uptake plotplot_chiclet
Peptide coverageplot_coverage
Coverage heatmapplot_coverage_heatmap
Differential plotplot_differential
Butterfly differential deuterium uptake plotplot_differential_butterfly
Chiclet differential deuterium uptake plotplot_differential_chiclet
Plot differential uptake curveplot_differential_uptake_curve
Manhattan plotplot_manhattan
Plot overlap dataplot_overlap
Plot overlap distributionplot_overlap_distribution
Plot peptide charge measurementplot_peptide_charge_measurement
Plot peptide mass measurementplot_peptide_mass_measurement
Position frequencyplot_position_frequency
Plot quality control dataplot_quality_control
Plot replicates histogramplot_replicate_histogram
Replicate mass uptake curveplot_replicate_mass_uptake
State deuterium uptake comparisonplot_state_comparison
Uncertainty of the peptide measurementsplot_uncertainty
Deuterium uptake curveplot_uptake_curve
Volcano plotplot_volcano
Prepares data export for HDX-Viewerprepare_hdxviewer_export
Read HDX-MS data fileread_hdx
Reconstruct protein sequencereconstruct_sequence
Show aggregated values in friendly formshow_aggregated_uptake_data
Coverage heatmap datashow_coverage_heatmap_data
Differential deuterium uptake datashow_diff_uptake_data
Differential uptake data with confidenceshow_diff_uptake_data_confidence
Show data on peptide overlapshow_overlap_data
Differential deuterium uptake datashow_p_diff_uptake_data
Show peptide charge measurementshow_peptide_charge_measurement
Show peptide mass measurementshow_peptide_mass_measurement
Show quality control datashow_quality_control_data
Show replicate datashow_replicate_histogram_data
Summary datashow_summary_data
Deuterium uptake curve datashow_uc_data
Deuterium uptake datashow_uptake_data
Update HDeXaminer datafileupdate_hdexaminer_file