safe
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see safe.
Significance Analysis of Function and Expression
Bioconductor version: 3.7
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: William T. Barry <bbarry at jimmy.harvard.edu>
citation("safe")
):
Installation
To install this package, start R (version "3.5") 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 | R Script | |
Reference Manual |
Details
biocViews | DifferentialExpression, GeneSetEnrichment, Pathways, Software, StatisticalMethod |
Version | 3.20.0 |
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 |
See More
Suggests | GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats |
Linking To | |
Enhances | |
Depends On Me | |
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_3.20.0.tar.gz |
Windows Binary | safe_3.20.0.zip |
Mac OS X 10.11 (El Capitan) | safe_3.20.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/safe |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/safe |
Package Short Url | https://bioconductor.org/packages/safe/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.7 | Source Archive |