Package: MsExperiment 1.15.0

Laurent Gatto

MsExperiment: Infrastructure for Mass Spectrometry Experiments

Infrastructure to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry (MS) experiment. The MsExperiment package provides light-weight and flexible containers for MS experiments building on the new MS infrastructure provided by the Spectra, QFeatures and related packages. Along with raw data representations, links to original data files and sample annotations, additional metadata or annotations can also be stored within the MsExperiment container. To guarantee maximum flexibility only minimal constraints are put on the type and content of the data within the containers.

Authors:Laurent Gatto [aut, cre], Johannes Rainer [aut], Sebastian Gibb [aut], Tuomas Borman [ctb]

MsExperiment_1.15.0.tar.gz
MsExperiment_1.15.0.zip(r-4.7-any)MsExperiment_1.15.0.zip(r-4.6-any)MsExperiment_1.15.0.zip(r-4.5-any)
MsExperiment_1.15.0.tgz(r-4.6-any)MsExperiment_1.15.0.tgz(r-4.5-any)
MsExperiment_1.15.0.tar.gz(r-4.7-any)MsExperiment_1.15.0.tar.gz(r-4.6-any)
MsExperiment_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MsExperiment/json (API)

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

Bug tracker:https://github.com/rformassspectrometry/msexperiment/issues

On BioConductor:MsExperiment-1.15.0(bioc 3.24)MsExperiment-1.14.0(bioc 3.23)

infrastructureproteomicsmassspectrometrymetabolomicsexperimentaldesigndataimport

8.01 score 5 stars 21 packages 284 scripts 2.9k downloads 19 exports 103 dependencies

Last updated from:e608756e18. Checks:8 WARNING, 1 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING201
linux-develWARNING406
source / vignettesERROR841
linux-releaseWARNING465
macos-releaseWARNING324
macos-oldrelWARNING327
windows-develWARNING440
windows-releaseWARNING414
windows-oldrelWARNING434
wasm-releaseOK148

Exports:dbWriteSampleDataexistMsExperimentFilesexperimentFilesexperimentFiles<-filterSpectralinkSampleDataMsExperimentMsExperimentFilesotherDataotherData<-qdataqdata<-readMsExperimentsampleDatasampleData<-showspectraspectra<-spectraSampleIndex

Dependencies:abindAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbslibcachemcliclueclustercodetoolscpp11crosstalkcurldata.tableDBIDelayedArraydigestdplyrevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMultiAssayExperimentopensslotelpillarpkgconfigplotlyplyrpromisesProtGenericspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Write sample annotations to a MsBackendSql SQL databasedbWriteSampleData
Managing Mass Spectrometry ExperimentsexperimentFiles experimentFiles<- filterSpectra,MsExperiment,function-method length,MsExperiment-method linkSampleData MsExperiment MsExperiment-class otherData otherData<- qdata qdata<- sampleData sampleData<- show,MsExperiment-method spectra,MsExperiment-method spectra<-,MsExperiment-method spectraSampleIndex [,MsExperiment,ANY,ANY,ANY-method
A class to store experiment filesexistMsExperimentFiles MsExperimentFiles MsExperimentFiles-class show,MsExperimentFiles-method
Import MS spectra data of an experimentreadMsExperiment