About HaDeX | Comparison of the existing HDX-MS software | HaDeX functionalities | Data import | Computation of deuteration levels | Measured data into overall peptide mass | Experimental deuteration level | Uncertainty calculations | Theoretical deuteration level | Difference of deuteration levels between two states | Visual data analysis | Comparison of states | Woods plot | Confidence limit in Woods plot | Kinetic plots | Additional tools | Peptide coverage | Quality control | HaDeX Graphical User Interface | Examples | Example 1: CD160-HVEM | Example workflow 2 | References
Package: HaDeX 1.2.3
HaDeX: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data
Functions for processing, analysis and visualization of Hydrogen Deuterium eXchange monitored by Mass Spectrometry experiments (HDX-MS) (<doi:10.1093/bioinformatics/btaa587>). 'HaDeX' introduces a new standardized and reproducible workflow for the analysis of the HDX-MS data, including novel uncertainty intervals. Additionally, it covers data exploration, quality control and generation of publication-quality figures. All functionalities are also available in the in-built 'Shiny' app.
Authors:
HaDeX_1.2.3.tar.gz
HaDeX_1.2.3.zip(r-4.7-any)HaDeX_1.2.3.zip(r-4.6-any)HaDeX_1.2.3.zip(r-4.5-any)
HaDeX_1.2.3.tgz(r-4.6-any)HaDeX_1.2.3.tgz(r-4.5-any)
HaDeX_1.2.3.tar.gz(r-4.7-any)HaDeX_1.2.3.tar.gz(r-4.6-any)
HaDeX_1.2.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
HaDeX/json (API)
| # Install 'HaDeX' in R: |
| install.packages('HaDeX', repos = c('https://werpuc.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:457d71e644. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 160 | ||
| source / vignettes | OK | 252 | ||
| linux-release | OK | 162 | ||
| macos-release | OK | 212 | ||
| macos-oldrel | OK | 195 | ||
| windows-devel | OK | 109 | ||
| windows-release | OK | 123 | ||
| windows-oldrel | OK | 108 | ||
| wasm-release | OK | 142 |
Exports:add_stat_dependencycalculate_confidence_limit_valuescalculate_kineticscalculate_state_deuterationcomparison_plotHaDeX_guiplot_coverageplot_kineticsplot_position_frequencyprepare_datasetquality_controlread_hdxreconstruct_sequencewoods_plot
Dependencies:base64encbitbit64bslibcachemcellrangerclicliprcommonmarkcpp11crayondata.tabledigestdplyrfarverfastmapfontawesomefsgenericsggplot2gluegtablehmshtmltoolshttpuvisobandjquerylibjsonlitelabelinglaterlatex2explifecyclemagrittrmemoisemimeotelpillarpkgconfigplyrprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrreadxlrematchreshape2rlangS7sassscalesshinysourcetoolsstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrxtable
Supplement to: "HaDeX: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data"
Last update: 2025-07-04
Started: 2021-08-12
Data aggregation
Aggregation of the data - visualization
Last update: 2021-08-12
Started: 2021-08-12
Data processing
Processing data from DynamX | Differences between files | Initial processing of the data | Calculation of the deuterium uptake | Deuterium uptake | Fractional deuterium uptake | Theoretical deuterium uptake | Theoretical fractional deuterium uptake | Differential values | Additional information
Last update: 2021-08-12
Started: 2021-08-12
Mass calculation
Comparison of results with weighted mean and without
Last update: 2021-08-12
Started: 2021-08-12
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| HaDeX | HaDeX-package HaDeX |
| Calculates confidence limits | add_stat_dependency |
| Calculate the value of confidence limit | calculate_confidence_limit_values |
| Calculate kinetic data | calculate_kinetics |
| Calculate deuteration | calculate_state_deuteration |
| Plot comparison plot | comparison_plot |
| HaDeX Graphical User Interface | HaDeX_gui |
| Plot peptide coverage | plot_coverage |
| Plot kinetics data | plot_kinetics |
| Plot position frequency | plot_position_frequency |
| Calculate data | prepare_dataset |
| Experiment quality control | quality_control |
| Read HDX-MS data file | read_hdx |
| Reconstruct protein sequence | reconstruct_sequence |
| Plot Woods' plot | woods_plot |