To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("safe")
In most cases, you don't need to download the package archive at all.
safe
Significance Analysis of Function and Expression
Bioconductor version: 3.0
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")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("safe")
Documentation
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 |
Details
| biocViews | DifferentialExpression, GeneSetEnrichment, Pathways, Software, StatisticalMethod |
| Version | 3.6.1 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier |
| 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 | EnrichmentBrowser |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | safe_3.6.1.tar.gz |
| Windows Binary | safe_3.6.1.zip |
| Mac OS X 10.6 (Snow Leopard) | safe_3.6.1.tgz |
| Mac OS X 10.9 (Mavericks) | safe_3.6.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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