safe

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see safe.

Significance Analysis of Function and Expression

Bioconductor version: 3.14

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.

Author: William T. Barry

Maintainer: Ludwig Geistlinger <ludwig_geistlinger at hms.harvard.edu>

Citation (from within R, enter citation("safe")):

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("safe")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("safe")

SAFE manual PDF R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, GeneSetEnrichment, Pathways, Software, StatisticalMethod

Version 3.34.0

In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)

License GPL (>= 2)

Depends R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM

Imports

System Requirements

URL

Suggests GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats

Linking To

Enhances

Depends On Me PCGSE

Imports Me EGSEA, EnrichmentBrowser

Suggests Me

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package safe_3.34.0.tar.gz

Windows Binary safe_3.34.0.zip

macOS 10.13 (High Sierra) safe_3.34.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/safe

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/safe

Bioc Package Browser https://code.bioconductor.org/browse/safe/

Package Short Url https://bioconductor.org/packages/safe/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.14 Source Archive