Package: HaDeX 1.2.2
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) (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_1.2.2.tar.gz
HaDeX_1.2.2.zip(r-4.5)HaDeX_1.2.2.zip(r-4.4)HaDeX_1.2.2.zip(r-4.3)
HaDeX_1.2.2.tgz(r-4.4-any)HaDeX_1.2.2.tgz(r-4.3-any)
HaDeX_1.2.2.tar.gz(r-4.5-noble)HaDeX_1.2.2.tar.gz(r-4.4-noble)
HaDeX_1.2.2.tgz(r-4.4-emscripten)HaDeX_1.2.2.tgz(r-4.3-emscripten)
HaDeX.pdf |HaDeX.html✨
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 3 years agofrom:3d10b96831. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 17 2024 |
| R-4.5-win | NOTE | Oct 17 2024 |
| R-4.5-linux | NOTE | Oct 17 2024 |
| R-4.4-win | NOTE | Oct 17 2024 |
| R-4.4-mac | NOTE | Oct 17 2024 |
| R-4.3-win | NOTE | Oct 17 2024 |
| R-4.3-mac | NOTE | Oct 17 2024 |
Exports:add_stat_dependencycalculate_confidence_limit_valuescalculate_kineticscalculate_state_deuterationcomparison_plotHaDeX_guiplot_coverageplot_kineticsplot_position_frequencyprepare_datasetquality_controlread_hdxreconstruct_sequencewoods_plot
Dependencies:base64encbitbit64bslibcachemcellrangerclicliprcolorspacecommonmarkcpp11crayoncrosstalkdata.tabledigestdplyrDTevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegsubfngtablehighrhmshtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatex2explatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigplyrprettyunitsprogresspromisesprotopurrrR6rappdirsRColorBrewerRcppreadrreadxlrematchreshape2rlangrmarkdownsassscalesshinysourcetoolsstringistringrtibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunxtableyaml
Data aggregation
Rendered fromtransformation.Rmdusingknitr::rmarkdownon Oct 17 2024.Last update: 2021-08-12
Started: 2021-08-12
Data processing
Rendered fromdatafiles.Rmdusingknitr::rmarkdownon Oct 17 2024.Last update: 2021-08-12
Started: 2021-08-12
Supplement to: "HaDeX: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data"
Rendered fromHaDeX.Rmdusingknitr::rmarkdownon Oct 17 2024.Last update: 2021-08-12
Started: 2021-08-12
Mass calculation
Rendered frommass_comparison.Rmdusingknitr::rmarkdownon Oct 17 2024.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 |
