Package: hdxmsqc 1.8.0

Oliver M. Crook

hdxmsqc: An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments

The hdxmsqc package enables us to analyse and visualise the quality of HDX-MS experiments. Either as a final quality check before downstream analysis and publication or as part of a interative procedure to determine the quality of the data. The package builds on the QFeatures and Spectra packages to integrate with other mass-spectrometry data.

Authors:Oliver M. Crook [aut, cre]

hdxmsqc_1.8.0.tar.gz
hdxmsqc_1.8.0.zip(r-4.7)hdxmsqc_1.8.0.zip(r-4.6)hdxmsqc_1.8.0.zip(r-4.5)
hdxmsqc_1.8.0.tgz(r-4.6-any)hdxmsqc_1.8.0.tgz(r-4.5-any)
hdxmsqc_1.8.0.tar.gz(r-4.7-any)hdxmsqc_1.8.0.tar.gz(r-4.6-any)
hdxmsqc_1.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
hdxmsqc/json (API)
NEWS

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

Bug tracker:https://github.com/ococrook/hdxmsqc/issues

Datasets:
  • BRD4df - This is data to be included in my package
  • BRD4df_full - This is data to be included in my package

On BioConductor:hdxmsqc-1.9.0(bioc 3.24)hdxmsqc-1.8.0(bioc 3.23)

qualitycontroldataimportproteomicsmassspectrometrymetabolomics

4.00 score 1 stars 5 scripts 260 downloads 23 exports 105 dependencies

Last updated from:5fcaeb4dc7 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR192
linux-devel-x86_64NOTE369
source / vignettesOK422
linux-release-x86_64NOTE390
macos-release-arm64NOTE179
macos-oldrel-arm64NOTE185
windows-develNOTE283
windows-releaseNOTE268
windows-oldrelNOTE248
wasm-releaseOK163

Exports:chargeCorrelationHdxcompatibleUptakecomputeMassErrorcomputeMonotoneStatsexchangeableAmidesfourierIsotopegenerateSpectraimTimeOutlierintensityOutliersisMissingAtRandomisotopicDistributionHDXfourierplotImTimeOutlierplotIntensityOutliersplotMassErrorplotMissingplotMonotoneStatplotrTimeOutliersprocessHDEqualityControlreplicateCorrelationreplicateOutlierrTimeOutliersspectraSimilarity

Dependencies:abindAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelBiocStylebookdownbslibcachemcliclueclustercodetoolscpp11crosstalkcurldata.tableDelayedArraydigestdplyrevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMultiAssayExperimentopensslotelpillarpkgconfigplotlyplyrpromisesProtGenericspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml

qc-tidying

Oliver M. Crook

Rendered fromqc-streamlined.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2024-06-30
Started: 2024-01-31

Readme and manuals

Help Manual

Help pageTopics
This is data to be included in my packageBRD4df
This is data to be included in my packageBRD4df_full
Charge states should have correlated incorperation but they need not be exactly the samechargeCorrelationHdx
Check whether deuterium uptakes are compatible with difference overlapping sequences.compatibleUptake
Empirical versus theoretical mass errorscomputeMassError
Monotonicity based outlier detection.computeMonotoneStats
Compute exchangeable amides.exchangeableAmides
fourier transform approach to computing isotopic distributionfourierIsotope
generate Spectra using a fourier transformgenerateSpectra
A package to perfrom quality control for mass-spectrometry based hydrogen deuterium exchange experiment.hdxmsqc
Ion Mobility time based outlier analysisimTimeOutlier
Intensity based deviationsintensityOutliers
Missing at random versus missing not at randomisMissingAtRandom
fourier transform approach to computing isotopic distributionisotopicDistributionHDXfourier
Ion Mobility time based outlier analysisplotImTimeOutlier
Intensity based deviation plotplotIntensityOutliers
Mass error plotplotMassError
missing value plotplotMissing
Monotonicity based outlier detection, plot.plotMonotoneStat
Retention time based analysisplotrTimeOutliers
Function to curate and HDExaminer file so that in contains all the information in a sensible format. This object can then be straightforwardly passed to a object of class 'QFeatures'processHDE
Quality Control table function. Generate a table that collates quality control metricsqualityControl
Correlation based checksreplicateCorrelation
Correlation based checksreplicateOutlier
Retention time based analysisrTimeOutliers
Spectral checking using data from HDsitespectraSimilarity