safe
This is the released version of safe; for the devel version, see safe.
Significance Analysis of Function and Expression
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 3.52.1 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 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_3.52.1.tar.gz |
| Windows Binary (x86_64) | safe_3.52.1.zip |
| macOS Binary (big-sur-x86_64) | safe_3.52.1.tgz |
| macOS Binary (sonoma-arm64) | safe_3.52.1.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 3.23 | Source Archive |