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
MsExperiment_1.9.1.zip(r-4.5)MsExperiment_1.9.1.zip(r-4.4)MsExperiment_1.5.5.zip(r-4.3)
MsExperiment_1.9.1.tgz(r-4.5-any)MsExperiment_1.9.1.tgz(r-4.4-any)MsExperiment_1.5.5.tgz(r-4.3-any)
MsExperiment_1.9.1.tar.gz(r-4.5-noble)MsExperiment_1.9.1.tar.gz(r-4.4-noble)
MsExperiment_1.9.1.tgz(r-4.4-emscripten)MsExperiment_1.9.1.tgz(r-4.3-emscripten)
MsExperiment.pdf |MsExperiment.html✨
MsExperiment/json (API)
NEWS

# Install 'MsExperiment' in R:
install.packages('MsExperiment', repos = c('https://rformassspectrometry.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

8.21 score 5 stars 14 packages 130 scripts 19 exports 109 dependencies

Last updated 11 days agofrom:bc06ba2278. Checks:1 OK, 5 NOTE, 2 FAILURE. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKFeb 11 2025
R-4.5-winNOTEFeb 11 2025
R-4.5-macNOTEFeb 11 2025
R-4.5-linuxNOTEFeb 11 2025
R-4.4-winNOTEFeb 11 2025
R-4.4-macNOTEFeb 11 2025
R-4.3-winOUTDATEDDec 12 2024
R-4.3-macOUTDATEDDec 12 2024

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

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

Managing Mass Spectrometry Experiments

Rendered fromMsExperiment.Rmdusingknitr::rmarkdownon Feb 11 2025.

Last update: 2024-04-16
Started: 2021-04-16

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