Package: limpca 1.9.0

Manon Martin

limpca: An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family of methods

This package has for objectives to provide a method to make Linear Models for high-dimensional designed data. limpca applies a GLM (General Linear Model) version of ASCA and APCA to analyse multivariate sample profiles generated by an experimental design. ASCA/APCA provide powerful visualization tools for multivariate structures in the space of each effect of the statistical model linked to the experimental design and contrarily to MANOVA, it can deal with mutlivariate datasets having more variables than observations. This method can handle unbalanced design.

Authors:Bernadette Govaerts [aut, ths], Sebastien Franceschini [ctb], Robin van Oirbeek [ctb], Michel Thiel [aut], Pascal de Tullio [dtc], Manon Martin [aut, cre], Nadia Benaiche [ctb]

limpca_1.9.0.tar.gz
limpca_1.9.0.zip(r-4.7)limpca_1.9.0.zip(r-4.6)limpca_1.9.0.zip(r-4.5)
limpca_1.9.0.tgz(r-4.6-any)limpca_1.9.0.tgz(r-4.5-any)
limpca_1.9.0.tar.gz(r-4.7-any)limpca_1.9.0.tar.gz(r-4.6-any)
limpca_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
limpca/json (API)
NEWS

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

Bug tracker:https://github.com/manonmartin/limpca/issues

Pkgdown/docs site:https://manonmartin.github.io

Datasets:
  • trout - Trout: the Rainbow trouts transcriptomic dataset
  • UCH - UCH: the Urine Citrate-Hippurate metabolomic dataset

On BioConductor:limpca-1.9.0(bioc 3.24)limpca-1.8.0(bioc 3.23)

statisticalmethodprincipalcomponentregressionvisualizationexperimentaldesignmultiplecomparisongeneexpressionmetabolomics

5.43 score 2 stars 5 scripts 246 downloads 22 exports 124 dependencies

Last updated from:eb4fa56366. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE264
linux-devel-x86_64OK380
source / vignettesOK352
linux-release-x86_64OK372
macos-release-arm64OK262
macos-oldrel-arm64OK205
windows-develOK313
windows-releaseOK327
windows-oldrelOK289
wasm-releaseOK180

Exports:data2LmpDataListlmpBootstrapTestslmpContributionslmpEffectMatriceslmpEffectPlotlmpLoading1dPlotlmpLoading2dPlotlmpModelMatrixlmpPcaEffectslmpScorePlotlmpScoreScatterPlotMlmpScreePlotpcaBySvdpcaLoading1dPlotpcaLoading2dPlotpcaScorePlotpcaScreePlotplotDesignplotLineplotMeansplotScatterplotScatterM

Dependencies:abindaskpassbackportsbase64encBiobaseBiocGenericsbitbit64blobbroombslibcachemcallrcellrangerclicliprcodetoolsconflictedcpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdoParalleldplyrdtplyrevaluatefarverfastmapfontawesomeforcatsforeachfsgarglegenericsGenomicRangesggplot2ggrepelggscigluegoogledrivegooglesheets4gtablehavenhighrhmshtmltoolshttridsIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclelubridatemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimemodelropensslpillarpkgconfigplyrprettyunitsprocessxprogresspspurrrR6raggrappdirsRColorBrewerRcppreadrreadxlrematchrematch2reprexreshape2rlangrmarkdownrstudioapirvestS4ArraysS4VectorsS7sassscalesselectrSeqinfoSparseArraystringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselecttidyversetimechangetinytextzdbutf8uuidvctrsviridisLitevroomwithrxfunxml2XVectoryaml

Application of limpca on the Trout transcriptomic dataset.

Benaiche Nadia, Bernadette Govaerts

Rendered fromTrout.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2024-04-26
Started: 2022-12-07

Application of limpca on the UCH metabolomics dataset.

Benaiche Nadia, Sébastien Franceschini, Martin Manon, Thiel Michel, Govaerts Bernadette

Rendered fromUCH.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2024-04-26
Started: 2022-09-20

Get started with limpca.

Benaiche Nadia, Sébastien Franceschini, Martin Manon, Thiel Michel, Govaerts Bernadette

Rendered fromlimpca.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2024-04-26
Started: 2022-12-06