Package: GOexpress
Title: Visualise microarray and RNAseq data using gene ontology
        annotations
Version: 1.45.0
Date: 2025-09-03
Authors@R: c(
    person(given="Kevin", family="Rue-Albrecht",
    role = c("aut", "cre"), email = "kevinrue67@gmail.com"),
    person(give=c("Tharvesh", "M.L."), family="Ali", role = c("ctb")),
    person(given=c("Paul", "A."), family="McGettigan", role = c("ctb")),
    person(given="Belinda", family="Hernandez", role = c("ctb")),
    person(given="David A.", family="Magee", role = c("ctb")),
    person(given="Nicolas C.", family="Nalpas", role = c("ctb")),
    person(given="Andrew", family="Parnell", role = c("ctb")),
    person(given=c("Stephen", "V."), family="Gordon", role = c("ths")),
    person(given=c("David", "E."), family="MacHugh", role = c("ths")),
    person(given="Hugo", family="Gruson", role = c("ctb")))
Description: 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.
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
License: GPL (>= 3)
biocViews: Software, GeneExpression, Transcription,
        DifferentialExpression, GeneSetEnrichment, DataRepresentation,
        Clustering, TimeCourse, Microarray, Sequencing, RNASeq,
        Annotation, MultipleComparison, Pathways, GO, Visualization,
        ImmunoOncology
URL: https://github.com/kevinrue/GOexpress
LazyData: true
Config/pak/sysreqs: make libicu-dev libpng-dev libxml2-dev libssl-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:21:33 UTC
RemoteUrl: https://github.com/bioc/GOexpress
RemoteRef: HEAD
RemoteSha: f14e6dfbcd79ebda5109863ad9b3908a92cdfad9
NeedsCompilation: no
Packaged: 2025-11-02 14:55:21 UTC; root
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]
Maintainer: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Built: R 4.6.0; ; 2025-11-02 14:56:50 UTC; windows
