GOexpress

DOI: 10.18129/B9.bioc.GOexpress    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see GOexpress.

Visualise microarray and RNAseq data using gene ontology annotations

Bioconductor version: 3.8

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]

Maintainer: Kevin Rue-Albrecht <kevinrue67 at gmail.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

PDF	R Script	UsersGuide
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Clustering, DataRepresentation, DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, MultipleComparison, Pathways, RNASeq, Sequencing, Software, TimeCourse, Transcription, Visualization
Version	1.16.1
In Bioconductor since	BioC 3.0 (R-3.1) (4.5 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)
LinkingTo
Suggests	BiocStyle
SystemRequirements
Enhances
URL	https://github.com/kevinrue/GOexpress
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GOexpress_1.16.1.tar.gz
Windows Binary	GOexpress_1.16.1.zip
Mac OS X 10.11 (El Capitan)	GOexpress_1.16.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GOexpress
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GOexpress
Package Short Url	http://bioconductor.org/packages/GOexpress/
Package Downloads Report	Download Stats