Package: gCMAPWeb
Type: Package
Title: A web interface for gene-set enrichment analyses
Version: 1.4.0
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, Rook
Imports: Biobase, annotate, AnnotationDbi, BiocGenerics, brew,
        graphics, grDevices, GSEABase, hwriter, IRanges, methods,
        parallel, stats, utils
Suggests: org.Hs.eg.db, org.Mm.eg.db, ArrayExpress, affy, hgfocus.db,
        ArrayExpress, hgu133a.db, mgug4104a.db, RUnit
Enhances: bigmemory, bigmemoryExtras
LazyLoad: yes
Packaged: 2014-04-12 10:17:32 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'
biocViews: GUI, GeneSetEnrichment, Visualization
Built: R 3.1.0; ; 2014-04-12 13:35:15 UTC; windows
