This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see safe.
Bioconductor version: 3.8
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 (from within R,
enter citation("safe")
):
To install this package, start R (version "3.5") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("safe")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("safe")
R Script | SAFE manual | |
Reference Manual |
biocViews | DifferentialExpression, GeneSetEnrichment, Pathways, Software, StatisticalMethod |
Version | 3.22.0 |
In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 14 years) |
License | GPL (>= 2) |
Depends | R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM |
Imports | |
LinkingTo | |
Suggests | GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | EGSEA, EnrichmentBrowser |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | safe_3.22.0.tar.gz |
Windows Binary | safe_3.22.0.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | safe_3.22.0.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 | http://bioconductor.org/packages/safe/ |
Package Downloads Report | Download Stats |
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