Bioconductor - GOexpress
Bioconductor 3.22
Software Packages
GOexpress
GOexpress
This is the
released
version of GOexpress; for the devel version, see
GOexpress
Visualise microarray and RNAseq data using gene ontology annotations
DOI:
10.18129/B9.bioc.GOexpress
Bioconductor version:
Release (3.22)
The package contains methods to visualise the expression profile of genes from a microarray or RNA-seq experiment, and offers a supervised clustering approach to identify GO terms containing genes with expression levels that best classify two or more predefined groups of samples. Annotations for the genes present in the expression dataset may be obtained from Ensembl through the biomaRt package, if not provided by the user. The default random forest framework is used to evaluate the capacity 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. P-values may be computed to assess the significance of GO term ranking. Visualisation function include gene expression profile, gene ontology-based heatmaps, and hierarchical clustering of experimental samples using gene expression data.
Author:
Kevin Rue-Albrecht [aut, cre], Tharvesh M.L. Ali [ctb], 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], Hugo Gruson [ctb]
Maintainer:
Kevin Rue-Albrecht
Citation (from within R, enter
citation("GOexpress")
):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GOexpress")
For older versions of R, please refer to the appropriate
Bioconductor release
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GOexpress")
UsersGuide
PDF
R Script
Reference Manual
PDF
NEWS
Text
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
Annotation
Clustering
DataRepresentation
DifferentialExpression
GO
GeneExpression
GeneSetEnrichment
ImmunoOncology
Microarray
MultipleComparison
Pathways
RNASeq
Sequencing
Software
TimeCourse
Transcription
Visualization
Version
1.44.0
In Bioconductor since
BioC 3.0 (R-3.1) (11.5 years)
License
GPL (>= 3)
Depends
R (>= 3.4), grid, stats, graphics,
Biobase
(>= 2.22.0)
Imports
biomaRt
(>= 2.18.0),
stringr
(>= 0.6.2),
ggplot2
(>= 0.9.0),
RColorBrewer
(>= 1.0),
gplots
(>= 2.13.0),
randomForest
(>= 4.6),
RCurl
(>= 1.95)
System Requirements
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instructions to use this package in your R session.
Source Package
GOexpress_1.44.0.tar.gz
Windows Binary (x86_64)
GOexpress_1.44.0.zip
macOS Binary (x86_64)
GOexpress_1.44.0.tgz
macOS Binary (arm64)
GOexpress_1.44.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/GOexpress
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/GOexpress
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