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)
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safe_3.53.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
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:

p53.stat - P53 Mutation Status

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.

differentialexpression pathways genesetenrichment statisticalmethod software

5.70 score 5 packages 42 scripts 4 mentions 26 exports 36 dependencies

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

Target	Result	Time
bioc-checks	ERROR	322
linux-devel-x86_64	NOTE	367
source / vignettes	OK	499
linux-release-x86_64	NOTE	312
macos-release-arm64	NOTE	155
macos-oldrel-arm64	NOTE	178
windows-devel	NOTE	212
windows-release	NOTE	215
windows-oldrel	NOTE	224
wasm-release	OK	233

Exports:error.FDR.BH error.FDR.YB error.FWER.Bonf error.FWER.Holm error.FWER.WY gene.results getCmatrix getCOXresiduals getPIcomplete getPImatrix getXYresiduals global.AveDiff global.Fisher global.Kolmogorov global.Pearson global.Wilcoxon local.f.ANOVA local.t.LM local.t.paired local.t.Student local.t.Welch safe safe.toptable safedag safeplot sigfig

Dependencies:AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI fastmap generics glue httr IRanges jsonlite KEGGREST lifecycle memoise mime openssl pkgconfig png R6 rlang RSQLite S4Vectors Seqinfo SparseM sys vctrs XVector

SAFE manual

Rendered fromSAFEmanual3.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Significance Analysis of Function and Expression	safe-package
Gene-specific results from SAFE	gene.results
Generation of a C matrix	getCmatrix
p53 Mutation Status	p53.stat
Significance Analysis of Function and Expression	safe
Class SAFE	SAFE-class show,SAFE-method [,SAFE-method
Category-specific results from SAFE	safe.toptable
SAFE results displayed in Gene Ontology	safedag
SAFE plot	safeplot