Package: GOexpress
Title: Visualise microarray and RNAseq data using gene ontology
        annotations
Version: 1.0.1
Date: 2014-10-17
Authors@R: c(
    person(given="Kevin", family="Rue-Albrecht",
    role = c("aut", "cre"), email = "kevin.rue@ucdconnect.ie"),
    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 levels
    of genes from a microarray or RNA-seq experiment and offers a clustering
    analysis to identify GO terms enriched in genes with expression levels
    best clustering two or more predefined groups of samples. Annotations for
    the genes present in the expression dataset are obtained from Ensembl
    through the biomaRt package. The random forest framework is used to
    evaluate the ability 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. An ANOVA approach is also available as an alternative
    statistical framework.
Depends: R (>= 3.0.2), grid, Biobase (>= 2.22.0)
Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0),
        RColorBrewer (>= 1.0), gplots (>= 2.13.0), VennDiagram (>=
        1.6.5), randomForest (>= 4.6)
License: GPL (>= 3)
biocViews: Software, GeneExpression, Transcription,
        DifferentialExpression, GeneSetEnrichment, DataRepresentation,
        Metagenomics, Clustering, TimeCourse, Microarray, Sequencing,
        RNASeq, Annotation, MultipleComparison, Pathways, GO,
        Visualization
URL: https://github.com/kevinrue/GOexpress-release
LazyData: true
Packaged: 2014-10-18 05:01:25 UTC; biocbuild
Author: Kevin Rue-Albrecht [aut, cre],
  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 <kevin.rue@ucdconnect.ie>
Built: R 3.1.1; ; 2014-10-18 08:55:53 UTC; windows
