safe
This is the development version of safe; for the stable release version, see safe.
Significance Analysis of Function and Expression
Bioconductor version: Development (3.22)
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 gmail.com>
citation("safe")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 3.49.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 20.5 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 | ReporterScore |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | safe_3.49.0.tar.gz |
| Windows Binary (x86_64) | safe_3.49.0.zip |
| macOS Binary (x86_64) | safe_3.49.0.tgz |
| macOS Binary (arm64) | safe_3.49.0.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 |