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

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'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.91 score 41 scripts 268 downloads 14 exports 88 dependencies

Last updated 3 years agofrom:3d10b96831. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-winNOTENov 16 2024
R-4.5-linuxNOTENov 16 2024
R-4.4-winNOTENov 16 2024
R-4.4-macNOTENov 16 2024
R-4.3-winNOTENov 16 2024
R-4.3-macNOTENov 16 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 Nov 16 2024.

Last update: 2021-08-12
Started: 2021-08-12

Data processing

Rendered fromdatafiles.Rmdusingknitr::rmarkdownon Nov 16 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 Nov 16 2024.

Last update: 2021-08-12
Started: 2021-08-12

Mass calculation

Rendered frommass_comparison.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2021-08-12
Started: 2021-08-12

Readme and manuals

Help Manual

Help pageTopics
HaDeXHaDeX-package HaDeX
Calculates confidence limitsadd_stat_dependency
Calculate the value of confidence limitcalculate_confidence_limit_values
Calculate kinetic datacalculate_kinetics
Calculate deuterationcalculate_state_deuteration
Plot comparison plotcomparison_plot
HaDeX Graphical User InterfaceHaDeX_gui
Plot peptide coverageplot_coverage
Plot kinetics dataplot_kinetics
Plot position frequencyplot_position_frequency
Calculate dataprepare_dataset
Experiment quality controlquality_control
Read HDX-MS data fileread_hdx
Reconstruct protein sequencereconstruct_sequence
Plot Woods' plotwoods_plot