gCMAPWeb

DOI: 10.18129/B9.bioc.gCMAPWeb    

This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see gCMAPWeb.

A web interface for gene-set enrichment analyses

Bioconductor version: 3.11

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.t at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("gCMAPWeb")

For older versions of R, please refer to the appropriate Bioconductor release.

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	DifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, Microarray, Software, Transcription, Visualization
Version	1.27.0
In Bioconductor since	BioC 2.12 (R-3.0) (7.5 years)
License	Artistic-2.0
Depends	Biobase, gCMAP(>= 1.3.0), methods, R (>= 3.4), Rook
Imports	brew, BiocGenerics, annotate, AnnotationDbi, graphics, grDevices, GSEABase, hwriter, parallel, stats, utils, 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
Links To Me
Build Report

Package Archives

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

Source Package	gCMAPWeb_1.27.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/gCMAPWeb
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/gCMAPWeb
Package Short Url	https://bioconductor.org/packages/gCMAPWeb/
Package Downloads Report	Download Stats