To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GSAR")
In most cases, you don't need to download the package archive at all.
GSAR
Gene Set Analysis in R
Bioconductor version: 3.0
Gene set analysis using specific alternative hypotheses. Tests for differential expression, scale and net correlation structure.
Author: Yasir Rahmatallah <yrahmatallah at uams.edu>, Galina Glazko <gvglazko at uams.edu>
Maintainer: Yasir Rahmatallah <yrahmatallah at uams.edu>, Galina Glazko <gvglazko at uams.edu>
Citation (from within R,
enter citation("GSAR")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GSAR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GSAR")
| R Script | Gene Set Analysis in R -- the GSAR Package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, Software, StatisticalMethod |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | GPL (>=2) |
| Depends | R (>= 3.0.1), igraph (>= 0.7.0) |
| Imports | |
| LinkingTo | |
| Suggests | MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | GSAR_1.0.0.tar.gz |
| Windows Binary | GSAR_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | GSAR_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | GSAR_1.0.0.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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