Visualise microarray and RNAseq data using gene ontology annotations

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Documentation for package ‘GOexpress’ version 1.40.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

GOexpress-package	Visualise microarray and RNAseq data with gene ontology annotations.
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 and gene features.
AlvMac_results	Sample output from the 'GO_analyse()' function on an RNAseq experiment.
AlvMac_results.pVal	Sample output from the 'pValue_GO()' function on an RNAseq experiment.
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 series
expression_profiles_symbol	Plots the individual expression profile of a gene in samples series
GOexpress	Visualise microarray and RNAseq data with gene ontology annotations.
GO_analyse	Identifies gene ontologies clustering samples according to predefined factor.
heatmap_GO	Generates a heatmap and hierarchical clustering of the samples and the genes
hist_scores	Plots the distribution of scores following an GOexpress analysis.
list_genes	Returns the genes associated with a Gene Ontology
microarray2dataset	Table mapping probeset identifier prefixes to datasets in the Ensembl BioMart.
plot_design	Plot Univariate Effects for genes associated with a Gene Ontology
prefix2dataset	Table mapping Ensembl gene identifier prefixes to BioMart datasets.
pValue_GO	Compute p-values for ontologies by randomising gene labels.
quantiles_scores	Returns the quantiles of scores following an GOexpress analysis.
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 Gene Ontology