GOexpress: Visualise microarray and RNAseq data using gene ontology annotations

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GOexpress")
AuthorKevin 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]
Bioconductor views Annotation Clustering DataRepresentation DifferentialExpression GO GeneExpression GeneSetEnrichment Microarray MultipleComparison Pathways RNASeq Sequencing Software TimeCourse Transcription Visualization
Date of publicationNone
MaintainerKevin Rue-Albrecht <kevinrue67@gmail.com>
LicenseGPL (>= 3)
Version1.10.0
https://github.com/kevinrue/GOexpress

View on Bioconductor

Man pages

AlvMac: Sample data from a RNAseq experiment.

AlvMac_allgenes: Example of custom gene feature annotations.

AlvMac_allGO: Example of custom gene ontology annotations.

AlvMac_GOgenes: Example of custom mapping between gene ontology identifiers...

AlvMac_results: Sample output from the 'GO_analyse()' function on an RNAseq...

AlvMac_results.pVal: Sample output from the 'pValue_GO()' function on an RNAseq...

cluster_GO: Generates a hierarchical clustering of the samples

expression_plot: Plots the expression profile of a gene by levels of a factor

expression_plot_symbol: Plots the expression profile of a gene by levels of a factor

expression_profiles: Plots the individual expression profile of a gene in samples...

expression_profiles_symbol: Plots the individual expression profile of a gene in samples...

GO_analyse: Identifies gene ontologies clustering samples according to...

GOexpress-package: Visualise microarray and RNAseq data with gene ontology...

heatmap_GO: Generates a heatmap and hierarchical clustering of the...

hist_scores: Plots the distribution of scores following an GOexpress...

list_genes: Returns the genes associated with a Gene Ontology

microarray2dataset: Table mapping probeset identifier prefixes to datasets in the...

plot_design: Plot Univariate Effects for genes associated with a Gene...

prefix2dataset: Table mapping Ensembl gene identifier prefixes to BioMart...

pValue_GO: Compute p-values for ontologies by randomising gene labels.

quantiles_scores: Returns the quantiles of scores following an GOexpress...

rerank: Reorder the result variable by alternative metrics.

subEset: Subset an ExpressionSet to values of phenotypic data columns.

subset_scores: Returns a filtered list from GO_analyse results.

table_genes: Returns a table listing the genes associated with a given...

Functions

AlvMac Man page
AlvMac_allgenes Man page
AlvMac_allGO Man page
AlvMac_GOgenes Man page
AlvMac_results Man page
AlvMac_results.pVal Man page
cluster_GO Man page
expression_plot Man page
expression_plot_symbol Man page
expression_profiles Man page
expression_profiles_symbol Man page
GO_analyse Man page
GOexpress Man page
GOexpress-package Man page
heatmap_GO Man page
hist_scores Man page
list_genes Man page
microarray2dataset Man page
plot_design Man page
prefix2dataset Man page
pValue_GO Man page
quantiles_scores Man page
rerank Man page
subEset Man page
subset_scores Man page
table_genes Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/analysis.R R/post_analysis.R R/toolkit.R
README.md
build
build/vignette.rds
data
data/AlvMac.RData
data/AlvMac_GOgenes.RData
data/AlvMac_allGO.RData
data/AlvMac_allgenes.RData
data/AlvMac_results.RData
data/AlvMac_results.pVal.RData
data/datalist
data/microarray2dataset.RData
data/prefix2dataset.RData
inst
inst/doc
inst/doc/GOexpress-UsersGuide.R
inst/doc/GOexpress-UsersGuide.Rnw
inst/doc/GOexpress-UsersGuide.pdf
man
man/AlvMac.Rd man/AlvMac_GOgenes.Rd man/AlvMac_allGO.Rd man/AlvMac_allgenes.Rd man/AlvMac_results.Rd man/AlvMac_results.pVal.Rd man/GO_analyse.Rd man/GOexpress-package.Rd man/cluster_GO.Rd man/expression_plot.Rd man/expression_plot_symbol.Rd man/expression_profiles.Rd man/expression_profiles_symbol.Rd man/heatmap_GO.Rd man/hist_scores.Rd man/list_genes.Rd man/microarray2dataset.Rd man/pValue_GO.Rd man/plot_design.Rd man/prefix2dataset.Rd man/quantiles_scores.Rd man/rerank.Rd man/subEset.Rd man/subset_scores.Rd man/table_genes.Rd
vignettes
vignettes/GOexpress-UsersGuide.Rnw
vignettes/images
vignettes/images/shiny_screenshot.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.