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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GOexpress")
In most cases, you don't need to download the package archive at all.
GOexpress
Visualise microarray and RNAseq data using gene ontology annotations
Bioconductor version: 3.0
The package contains methods to visualise the expression levels of genes from a microarray or RNA-seq experiment and offers a clustering analysis to identify GO terms enriched in genes with expression levels best clustering two or more predefined groups of samples. Annotations for the genes present in the expression dataset are obtained from Ensembl through the biomaRt package. The random forest framework is used to evaluate the ability of each gene to cluster samples according to the factor of interest. Finally, GO terms are scored by averaging the rank (alternatively, score) of their respective gene sets to cluster the samples. An ANOVA approach is also available as an alternative statistical framework.
Author: Kevin Rue-Albrecht [aut, cre], Paul A. McGettigan [ctb], Belinda Hernandez [ctb], David A. Magee [ctb], Nicolas C. Nalpas [ctb], Andrew Parnell [ctb], Stephen V. Gordon [ths], David E. MacHugh [ths]
Maintainer: Kevin Rue-Albrecht <kevin.rue at ucdconnect.ie>
Citation (from within R,
enter citation("GOexpress")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GOexpress")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GOexpress")
| R Script | UsersGuide | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, Clustering, DataRepresentation, DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, Metagenomics, Microarray, MultipleComparison, Pathways, RNASeq, Sequencing, Software, TimeCourse, Transcription, Visualization |
| Version | 1.0.1 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | GPL (>= 3) |
| Depends | R (>= 3.0.2), grid, Biobase(>= 2.22.0) |
| Imports | biomaRt(>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), VennDiagram (>= 1.6.5), randomForest (>= 4.6) |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/kevinrue/GOexpress-release |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | GOexpress_1.0.1.tar.gz |
| Windows Binary | GOexpress_1.0.1.zip |
| Mac OS X 10.6 (Snow Leopard) | GOexpress_1.0.1.tgz |
| Mac OS X 10.9 (Mavericks) | GOexpress_1.0.1.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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