Package: GOexpress
Title: Visualise microarray and RNAseq data using gene ontology
        annotations
Version: 1.34.0
Date: 2017-04-04
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")))
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
git_url: https://git.bioconductor.org/packages/GOexpress
git_branch: RELEASE_3_17
git_last_commit: 3db4c6e
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
NeedsCompilation: no
Packaged: 2023-04-25 21:15:33 UTC; biocbuild
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@gmail.com>
Built: R 4.3.1; ; 2023-08-23 20:27:27 UTC; unix
