GOexpress
Visualise microarray and RNAseq data using gene ontology annotations
Bioconductor version: Release (3.20)
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>
citation("GOexpress")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("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")| UsersGuide | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Clustering, DataRepresentation, DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, MultipleComparison, Pathways, RNASeq, Sequencing, Software, TimeCourse, Transcription, Visualization |
| Version | 1.40.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (10 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) |
| System Requirements | |
| URL | https://github.com/kevinrue/GOexpress |
See More
| Suggests | BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | InteractiveComplexHeatmap |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GOexpress_1.40.0.tar.gz |
| Windows Binary (x86_64) | GOexpress_1.40.0.zip (64-bit only) |
| macOS Binary (x86_64) | GOexpress_1.40.0.tgz |
| macOS Binary (arm64) | GOexpress_1.40.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GOexpress |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GOexpress |
| Bioc Package Browser | https://code.bioconductor.org/browse/GOexpress/ |
| Package Short Url | https://bioconductor.org/packages/GOexpress/ |
| Package Downloads Report | Download Stats |