Package: safe 3.47.0

Ludwig Geistlinger

safe: Significance Analysis of Function and Expression

SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.

Authors:William T. Barry

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safe/json (API)

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

Peer review:

Datasets:

On BioConductor:safe-3.47.0(bioc 3.21)safe-3.46.0(bioc 3.20)

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

differentialexpressionpathwaysgenesetenrichmentstatisticalmethodsoftware

5.86 score 6 packages 49 scripts 1.0k downloads 4 mentions 26 exports 39 dependencies

Last updated 23 days agofrom:540d0be1bc. Checks:OK: 1 NOTE: 4 WARNING: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:error.FDR.BHerror.FDR.YBerror.FWER.Bonferror.FWER.Holmerror.FWER.WYgene.resultsgetCmatrixgetCOXresidualsgetPIcompletegetPImatrixgetXYresidualsglobal.AveDiffglobal.Fisherglobal.Kolmogorovglobal.Pearsonglobal.Wilcoxonlocal.f.ANOVAlocal.t.LMlocal.t.pairedlocal.t.Studentlocal.t.Welchsafesafe.toptablesafedagsafeplotsigfig

Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlifecyclememoisemimeopensslpkgconfigplogrpngR6rlangRSQLiteS4VectorsSparseMsysUCSC.utilsvctrsXVectorzlibbioc

SAFE manual

Rendered fromSAFEmanual3.Rnwusingutils::Sweaveon Oct 31 2024.

Last update: 2017-06-05
Started: 2013-01-10