Package: PAA 1.41.0

Michael Turewicz

PAA: PAA (Protein Array Analyzer)

PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the "minimum M statistic" approach - hereinafter referred to as "mMs"). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.

Authors:Michael Turewicz [aut, cre], Martin Eisenacher [ctb, cre]

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PAA.pdf |PAA.html✨
PAA/json (API)
NEWS

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

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:PAA-1.41.0(bioc 3.21)PAA-1.40.0(bioc 3.20)

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

classificationmicroarrayonechannelproteomicscpp

4.34 score 11 scripts 250 downloads 19 mentions 19 exports 78 dependencies

Last updated 2 months agofrom:e9dd570fad. Checks:OK: 1 NOTE: 5 ERROR: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-win-x86_64ERRORDec 19 2024
R-4.5-linux-x86_64NOTEDec 19 2024
R-4.4-win-x86_64ERRORDec 19 2024
R-4.4-mac-x86_64NOTEDec 19 2024
R-4.4-mac-aarch64NOTEDec 19 2024
R-4.3-win-x86_64ERRORDec 19 2024
R-4.3-mac-x86_64NOTEDec 19 2024
R-4.3-mac-aarch64NOTEDec 19 2024

Exports:batchAdjustbatchFilterbatchFilter.anovadiffAnalysisloadGPRmMsMatrixnormalizeArraysplotArrayplotFeaturesplotFeaturesHeatmapplotFeaturesHeatmap.2plotMAPlotsplotNormMethodspreselectprintFeaturespvaluePlotselectFeaturesshuffleDatavolcanoPlot

Dependencies:annotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobcachemcaToolsclassclicodetoolscpp11crayoncurlDBIe1071edgeRfastmapformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDatagluegplotsgtoolshttrigraphIRangesjsonliteKEGGRESTKernSmoothlambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemRMRenlmeopensslpkgconfigplogrpngproxyR6randomForestRcpprlangROCRRSQLiteS4VectorssnowstatmodsurvivalsvasysUCSC.utilsvctrsXMLxtableXVectorzlibbioc

PAA tutorial

Rendered fromPAA_vignette.Rnwusingutils::Sweaveon Dec 19 2024.

Last update: 2018-08-30
Started: 2014-10-03