To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("gCMAPWeb")

In most cases, you don't need to download the package archive at all.

gCMAPWeb

 

A web interface for gene-set enrichment analyses

Bioconductor version: Release (3.1)

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.

Author: Thomas Sandmann

Maintainer: Thomas Sandmann <sandmann.thomas at gene.com>

Citation (from within R, enter citation("gCMAPWeb")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("gCMAPWeb")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("gCMAPWeb")

 

PDF R Script gCMAPWeb configuration
PDF R Script Recreating the Broad Connectivity Map v1
PDF   Reference Manual
Text   NEWS

Details

biocViews GUI, GeneSetEnrichment, Software, Visualization
Version 1.8.0
In Bioconductor since BioC 2.12 (R-3.0) (2 years)
License Artistic-2.0
Depends Biobase, gCMAP(>= 1.3.0), methods, R (>= 2.15.0), Rook
Imports brew, BiocGenerics, annotate, AnnotationDbi, grDevices, GSEABase, hwriter, parallel, yaml
LinkingTo
Suggests affy, ArrayExpress, hgfocus.db, hgu133a.db, mgug4104a.db, org.Hs.eg.db, org.Mm.eg.db, RUnit
SystemRequirements
Enhances bigmemory, bigmemoryExtras
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source gCMAPWeb_1.8.0.tar.gz
Windows Binary gCMAPWeb_1.8.0.zip
Mac OS X 10.6 (Snow Leopard) gCMAPWeb_1.8.0.tgz
Mac OS X 10.9 (Mavericks) gCMAPWeb_1.8.0.tgz
Browse/checkout source (username/password: readonly)
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