Package: msmsTests 1.45.0
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:
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msmsTests.pdf |msmsTests.html✨
msmsTests/json (API)
| # Install 'msmsTests' in R: |
| install.packages('msmsTests', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- msms.spk - Yeast lisate samples spiked with human proteins
On BioConductor:msmsTests-1.45.0(bioc 3.21)msmsTests-1.44.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologysoftwaremassspectrometryproteomics
Last updated 4 months agofrom:0615a12562. Checks:1 OK, 6 NOTE, 1 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 28 2025 |
| R-4.5-win | NOTE | Jan 28 2025 |
| R-4.5-mac | WARNING | Jan 28 2025 |
| R-4.5-linux | NOTE | Jan 28 2025 |
| R-4.4-win | NOTE | Jan 28 2025 |
| R-4.4-mac | NOTE | Jan 28 2025 |
| R-4.3-win | NOTE | Jan 28 2025 |
| R-4.3-mac | NOTE | Jan 28 2025 |
Exports:msms.edgeRmsms.glm.poismsms.glm.qlllpval.by.fcres.volcanoplottest.results
Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbitopsbslibcachemcaToolscliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdoParalleldplyredgeRevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMALDIquantMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMsCoreUtilsmsmsEDAMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmeopensslpcaMethodspillarpkgconfigplotlyplyrpreprocessCorepromisesProtGenericsPSMatchpurrrQFeaturesqvalueR6rappdirsRColorBrewerRcppreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitevsnwithrxfunXMLXVectoryaml
msmsTests: controlling batch effects by blocking
Rendered frommsmsTests-Vignette2.Rnwusingutils::Sweaveon Jan 28 2025.Last update: 2013-11-01
Started: 2013-11-01
msmsTests: post test filters to improve reproducibility
Rendered frommsmsTests-Vignette.Rnwusingutils::Sweaveon Jan 28 2025.Last update: 2013-11-01
Started: 2013-11-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| LC-MS/MS Differential Expression Tests | msmsTests-package msmsTests |
| Spectral counts differential expression by edgeR | msms.edgeR |
| Spectral counts differential expression by Poisson GLM | msms.glm.pois |
| Spectral counts differential expression by quasi-likelihood GLM | msms.glm.qlll |
| Yeast lisate samples spiked with human proteins | msms.spk |
| Table of cumulative frequencies of p-values by log fold change bins | pval.by.fc |
| Volcanoplot | res.volcanoplot |
| Multitest p-value adjustment and post-test filter | test.results |
