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("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 | R Script | |
| Reference Manual |
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 |
See More
| 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 [email protected]: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 |