Package: gCMAPWeb
Type: Package
Title: A web interface for gene-set enrichment analyses
Version: 1.2.0
Author: Thomas Sandmann
Maintainer: Thomas Sandmann <sandmann.thomas@gene.com>
Description: The gCMAPWeb R package provides a graphical user interface for the
    gCMAP package. gCMAPWeb uses the Rook package and can be used either on a
    local machine, leveraging R's internal web server, or run on a dedicated
    rApache web server installation. gCMAPWeb allows users to search their own
    data sources and instructions to generate reference datasets from public
    repositories are included with the package. The package supports three
    common types of analyses, specifically queries with 1. one or two sets of
    query gene identifiers, whose members are expected to show changes in gene
    expression in a consistent direction. For example, an up-regulated gene set
    might contain genes activated by a transcription factor, a down-regulated
    geneset targets repressed by the same factor. 2. a single set of query gene
    identifiers, whose members are expected to show divergent differential
    expression (non-directional query). For example, members of a particular
    signaling pathway, some of which may be up- some down-regulated in response
    to a stimulus. 3. a query with the complete results of a differential
    expression profiling experiment. For example, gene identifiers and z-scores
    from a previous perturbation experiment. gCMAPWeb accepts three types of
    identifiers: EntreIds, gene Symbols and microarray probe ids and can be
    configured to work with any species supported by Bioconductor. For each
    query submission, significantly similar reference datasets will be
    identified and reported in graphical and tabular form.
License: Artistic-2.0
Depends: brew, gCMAP (>= 1.3.0), R (>= 2.15.0), yaml
Imports: Biobase, annotate, AnnotationDbi, BiocGenerics, brew,
        graphics, grDevices, GSEABase, hwriter, IRanges, methods,
        parallel, Rook, stats, utils
Suggests: org.Hs.eg.db, org.Mm.eg.db, ArrayExpress, affy, hgfocus.db,
        ArrayExpress, hgu133a.db, mgug4104a.db, RUnit
Enhances: bigmemory, bigmemoryExtras
biocViews: Bioinformatics, GUI, GeneSetEnrichment, Visualization
LazyLoad: yes
Packaged: 2013-10-15 08:15:04 UTC; biocbuild
Collate: 'gCMAPWeb-package.R' 'AllGenerics.R' 'cmapRun-methods.R'
        'cmap.R' 'cmapAnalysis.R' 'cmapHeatmap.R' 'createObject.R'
        'example_objects.R' 'file_io.R' 'html_elements.R'
        'plotting_functions.R' 'reporting.R'
Built: R 3.0.2; ; 2013-10-15 15:17:46 UTC; windows
