safe
Significance Analysis of Function and Expression
Bioconductor version: 2.10
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 <bill.barry at duke.edu>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("safe")
To cite this package in a publication, start R and enter:
citation("safe")
Documentation
| R Script | SAFE manual | |
| Reference Manual |
Details
| biocViews | FunctionalAnnotation, GeneExpression, Software |
| Depends | R (>= 2.4.0), Biobase, annotate, methods |
| Imports | SparseM, GO.db, annotate, AnnotationDbi, survival, Biobase |
| Suggests | GO.db, GOstats, Rgraphviz, multtest, hu6800.db, survival |
| System Requirements | |
| License | GPL (>= 2) |
| URL | http://www.duke.edu/~dinbarry/SAFE/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Version | 2.16.0 |
| Since | Bioconductor 1.6 (R-2.1) or earlier |
Package Downloads
| Package Source | safe_2.16.0.tar.gz |
| Windows Binary | safe_2.16.0.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) binary | safe_2.16.0.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Annotation
- Variants
- Flow Cytometry and other assays
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