Package: safe 3.53.1

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

safe_3.53.1.tar.gz
safe_3.53.1.zip(r-4.7)safe_3.53.1.zip(r-4.6)safe_3.53.1.zip(r-4.5)
safe_3.53.1.tgz(r-4.6-any)safe_3.53.1.tgz(r-4.5-any)
safe_3.53.1.tar.gz(r-4.7-any)safe_3.53.1.tar.gz(r-4.6-any)
safe_3.53.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
safe/json (API)

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

On BioConductor:safe-3.53.1(bioc 3.24)safe-3.52.1(bioc 3.23)

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

differentialexpressionpathwaysgenesetenrichmentstatisticalmethodsoftware

5.87 score 5 packages 62 scripts 890 downloads 4 mentions 26 exports 36 dependencies

Last updated from:cbf9c648ab. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR234
linux-devel-x86_64NOTE277
source / vignettesOK622
linux-release-x86_64NOTE314
macos-release-arm64NOTE392
macos-oldrel-arm64NOTE181
windows-develNOTE246
windows-releaseNOTE208
windows-oldrelNOTE218
wasm-releaseOK233

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:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsgluehttrIRangesjsonliteKEGGRESTlifecyclememoisemimeopensslpkgconfigpngR6rlangRSQLiteS4VectorsSeqinfoSparseMsysvctrsXVector

SAFE manual

Rendered fromSAFEmanual3.Rnwusingutils::Sweaveon Jun 01 2026.

Last update: 2026-05-01
Started: 2013-01-10