Package: GOexpress 1.41.0

Kevin Rue-Albrecht

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.

Authors: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]

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GOexpress.pdf |GOexpress.html✨
GOexpress/json (API)
NEWS

# Install 'GOexpress' in R:
install.packages('GOexpress', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/kevinrue/goexpress/issues

Datasets:
  • AlvMac - Sample data from a RNAseq experiment.
  • AlvMac_GOgenes - Example of custom mapping between gene ontology identifiers and gene features.
  • AlvMac_allGO - Example of custom gene ontology annotations.
  • AlvMac_allgenes - Example of custom gene feature annotations.
  • 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.
  • microarray2dataset - Table mapping probeset identifier prefixes to datasets in the Ensembl BioMart.
  • prefix2dataset - Table mapping Ensembl gene identifier prefixes to BioMart datasets.

On BioConductor:GOexpress-1.41.0(bioc 3.21)GOexpress-1.40.0(bioc 3.20)

softwaregeneexpressiontranscriptiondifferentialexpressiongenesetenrichmentdatarepresentationclusteringtimecoursemicroarraysequencingrnaseqannotationmultiplecomparisonpathwaysgovisualizationimmunooncologybioconductorbioconductor-packagebioconductor-statsgeneontologygeneset-enrichment

6.75 score 9 stars 31 scripts 240 downloads 4 mentions 16 exports 84 dependencies

Last updated 25 days agofrom:015022e824. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxWARNINGOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:cluster_GOexpression_plotexpression_plot_symbolexpression_profilesexpression_profiles_symbolGO_analyseheatmap_GOhist_scoreslist_genesplot_designpValue_GOquantiles_scoresreranksubEsetsubset_scorestable_genes

Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64bitopsblobcachemcaToolsclicolorspacecpp11crayoncurlDBIdbplyrdigestdplyrfansifarverfastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegplotsgtablegtoolshmshttrhttr2IRangesisobandjsonliteKEGGRESTKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6randomForestrappdirsRColorBrewerRCurlrlangRSQLiteS4VectorsscalesstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrxml2XVectorzlibbioc

UsersGuide

Rendered fromGOexpress-UsersGuide.Rnwusingutils::Sweaveon Oct 31 2024.

Last update: 2018-07-20
Started: 2014-09-27

Readme and manuals

Help Manual

Help pageTopics
Visualise microarray and RNAseq data with gene ontology annotations.GOexpress-package GOexpress
Sample data from a RNAseq experiment.AlvMac
Example of custom gene feature annotations.AlvMac_allgenes
Example of custom gene ontology annotations.AlvMac_allGO
Example of custom mapping between gene ontology identifiers and gene features.AlvMac_GOgenes
Sample output from the 'GO_analyse()' function on an RNAseq experiment.AlvMac_results
Sample output from the 'pValue_GO()' function on an RNAseq experiment.AlvMac_results.pVal
Generates a hierarchical clustering of the samplescluster_GO
Plots the expression profile of a gene by levels of a factorexpression_plot
Plots the expression profile of a gene by levels of a factorexpression_plot_symbol
Plots the individual expression profile of a gene in samples seriesexpression_profiles
Plots the individual expression profile of a gene in samples seriesexpression_profiles_symbol
Identifies gene ontologies clustering samples according to predefined factor.GO_analyse
Generates a heatmap and hierarchical clustering of the samples and the genesheatmap_GO
Plots the distribution of scores following an GOexpress analysis.hist_scores
Returns the genes associated with a Gene Ontologylist_genes
Table mapping probeset identifier prefixes to datasets in the Ensembl BioMart.microarray2dataset
Plot Univariate Effects for genes associated with a Gene Ontologyplot_design
Table mapping Ensembl gene identifier prefixes to BioMart datasets.prefix2dataset
Compute p-values for ontologies by randomising gene labels.pValue_GO
Returns the quantiles of scores following an GOexpress analysis.quantiles_scores
Reorder the result variable by alternative metrics.rerank
Subset an ExpressionSet to values of phenotypic data columns.subEset
Returns a filtered list from GO_analyse results.subset_scores
Returns a table listing the genes associated with a given Gene Ontologytable_genes