Package: msmsTests 1.51.0

Josep Gregori i Font

msmsTests: LC-MS/MS Differential Expression Tests

Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.

Authors:Josep Gregori, Alex Sanchez, and Josep Villanueva

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manual.pdf |manual.html✨
card.svg |card.png
msmsTests/json (API)

# Install 'msmsTests' in R:
install.packages('msmsTests', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • msms.spk - Yeast lisate samples spiked with human proteins

On BioConductor:msmsTests-1.51.0(bioc 3.24)msmsTests-1.50.0(bioc 3.23)

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

immunooncologysoftwaremassspectrometryproteomics

5.02 score 1 packages 22 scripts 688 downloads 4 mentions 6 exports 135 dependencies

Last updated from:36efb3a941. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR196
linux-devel-x86_64WARNING373
source / vignettesOK295
linux-release-x86_64WARNING310
macos-release-arm64WARNING174
macos-oldrel-arm64WARNING148
windows-develWARNING245
windows-releaseWARNING277
windows-oldrelWARNING265
wasm-releaseOK168

Exports:msms.edgeRmsms.glm.poismsms.glm.qlllpval.by.fcres.volcanoplottest.results

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocManagerBiocParallelbitopsbslibcachemcaToolscliclueclustercodetoolscpp11crosstalkcurldata.tableDelayedArraydigestdir.expirydoParalleldplyredgeRevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMALDIquantMASSMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsmsmsEDAMSnbaseMultiAssayExperimentmzIDmzRncdf4opensslotelpcaMethodspillarpkgconfigplotlyplyrpreprocessCorepromisesProtGenericsPSMatchPTModspurrrQFeaturesqvalueR6rappdirsRColorBrewerRcppreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitevsnwithrxfunXMLXVectoryaml

msmsTests: controlling batch effects by blocking

Rendered frommsmsTests-Vignette2.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2013-11-01
Started: 2013-11-01

msmsTests: post test filters to improve reproducibility

Rendered frommsmsTests-Vignette.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2013-11-01
Started: 2013-11-01