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biocLite("globaltest")
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globaltest
Testing groups of covariates/features for association with a response variable, with applications to gene set testing
Bioconductor version: 3.0
The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.
Author: Jelle Goeman and Jan Oosting, with contributions by Livio Finos and Aldo Solari
Maintainer: Jelle Goeman <j.j.goeman at lumc.nl>
Citation (from within R,
enter citation("globaltest")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("globaltest")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("globaltest")
| R Script | Global Test | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, GO, Microarray, OneChannel, Pathways, Software |
| Version | 5.20.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier |
| License | GPL (>= 2) |
| Depends | methods |
| Imports | Biobase, survival, AnnotationDbi, annotate, multtest, graphics |
| LinkingTo | |
| Suggests | vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, annotate, Biobase, survival, GSEABase, penalized, gss, MASS, boot, rpart |
| SystemRequirements | |
| Enhances | |
| URL | http://www.msbi.nl/goeman |
| Depends On Me | GlobalAncova |
| Imports Me | BiSeq, SIM |
| Suggests Me | topGO |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | globaltest_5.20.0.tar.gz |
| Windows Binary | globaltest_5.20.0.zip |
| Mac OS X 10.6 (Snow Leopard) | globaltest_5.20.0.tgz |
| Mac OS X 10.9 (Mavericks) | globaltest_5.20.0.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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