GOexpress
Visualise microarray and RNAseq data using gene ontology annotations
Bioconductor version: 3.24 · Package version: 1.47.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GOexpress")Details
| Maintainer | Kevin Rue-Albrecht <kevinrue67@gmail.com> |
| 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] |
| License | GPL (>= 3) |
| URL | https://github.com/kevinrue/GOexpress |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, Clustering, DataRepresentation, DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, MultipleComparison, Pathways, RNASeq, Sequencing, Software, TimeCourse, Transcription, Visualization |
| Package Short Url | https://bioconductor.org/packages/GOexpress/ |
Citation
From within R, enter citation("GOexpress"):
Kevin Rue-Albrecht. GOexpress: Visualise microarray and RNAseq data using gene ontology annotations. doi:10.18129/B9.bioc.GOexpress, R package version 1.47.0, https://bioconductor.org/packages/GOexpress.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | GOexpress_1.47.0.tar.gz |
| Windows binary (x86_64) | GOexpress_1.47.0.zip |
| macOS binary (arm64) | GOexpress_1.47.0.tgz |
| macOS binary (x86_64) | GOexpress_1.47.0.tgz |
Dependencies
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)
Suggests: BiocStyle
Reverse dependencies
Suggests Me (1): InteractiveComplexHeatmap