Package: MsExperiment 1.9.1

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]

MsExperiment_1.9.1.tar.gz
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MsExperiment.pdf |MsExperiment.html✨
MsExperiment/json (API)
NEWS

# 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-1.9.0(bioc 3.21)MsExperiment-1.8.0(bioc 3.20)

infrastructureproteomicsmassspectrometrymetabolomicsexperimentaldesigndataimport

7.51 score 5 stars 14 packages 126 scripts 2.0k downloads 19 exports 109 dependencies

Last updated 10 days agofrom:bc06ba2278. Checks:1 ERROR, 6 WARNING, 1 FAILURE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesFAILFeb 12 2025
R-4.5-winWARNINGFeb 12 2025
R-4.5-macWARNINGFeb 12 2025
R-4.5-linuxWARNINGFeb 12 2025
R-4.4-winWARNINGFeb 12 2025
R-4.4-macWARNINGFeb 12 2025
R-4.3-winWARNINGFeb 12 2025
R-4.3-macOUTDATEDJan 28 2025

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

Dependencies:abindAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbslibcachemcliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdplyrevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmgcvmimeMsCoreUtilsMultiAssayExperimentmunsellnlmeopensslpillarpkgconfigplotlyplyrpromisesProtGenericspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4ArraysS4VectorssassscalessnowSparseArraySpectrastringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryaml

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