Package: gCMAPWeb
Type: Package
Title: A web interface for gene-set enrichment analyses
Version: 1.14.0
Author: Thomas Sandmann
Maintainer: Thomas Sandmann <sandmann.t@gmail.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.
Note: gCMAPWeb is not compatible with the RStudio IDE, but can be used
        from the command line or via R's standard GUI.
License: Artistic-2.0
Depends: Biobase, gCMAP (>= 1.3.0), methods, R (>= 3.3.0), Rook
Imports: brew, BiocGenerics, annotate, AnnotationDbi, grDevices,
        GSEABase, hwriter, parallel, yaml
Suggests: affy, ArrayExpress, hgfocus.db, hgu133a.db, mgug4104a.db,
        org.Hs.eg.db, org.Mm.eg.db, RUnit
Enhances: bigmemory, bigmemoryExtras
biocViews: GUI, GeneSetEnrichment, Visualization
LazyLoad: yes
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'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-10-17 23:35:18 UTC; biocbuild
Built: R 3.3.1; ; 2016-10-18 02:28:53 UTC; windows
