gCMAP

Tools for Connectivity Map-like analyses

Bioconductor version: Release (2.14)

The gCMAP package provides a toolkit for comparing differential gene expression profiles through gene set enrichment analysis. Starting from normalized microarray or RNA-seq gene expression values (stored in lists of ExpressionSet and CountDataSet objects) the package performs differential expression analysis using the limma or DESeq packages. Supplying a simple list of gene identifiers, global differential expression profiles or data from complete experiments as input, users can use a unified set of several well-known gene set enrichment analysis methods to retrieve experiments with similar changes in gene expression. To take into account the directionality of gene expression changes, gCMAPQuery introduces the SignedGeneSet class, directly extending GeneSet from the GSEABase package. To increase performance of large queries, multiple gene sets are stored as sparse incidence matrices within CMAPCollection eSets. gCMAP offers implementations of 1. Fisher's exact test (Fisher, J R Stat Soc, 1922) 2. The "connectivity map" method (Lamb et al, Science, 2006) 3. Parametric and non-parametric t-statistic summaries (Jiang & Gentleman, Bioinformatics, 2007) and 4. Wilcoxon / Mann-Whitney rank sum statistics (Wilcoxon, Biometrics Bulletin, 1945) as well as wrappers for the 5. camera (Wu & Smyth, Nucleic Acid Res, 2012) 6. mroast and romer (Wu et al, Bioinformatics, 2010) functions from the limma package and 7. wraps the gsea method from the mgsa package (Bauer et al, NAR, 2010). All methods return CMAPResult objects, an S4 class inheriting from AnnotatedDataFrame, containing enrichment statistics as well as annotation data and providing simple high-level summary plots.

Author: Thomas Sandmann <sandmann.thomas at gene.com>, Richard Bourgon <bourgon.richard at gene.com> and Sarah Kummerfeld <kummerfeld.sarah at gene.com>

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

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("gCMAP")

Documentation

PDF R Script Creating reference datasets
PDF R Script gCMAP classes and methods
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, Microarray, Pathways, Software
Version 1.8.0
In Bioconductor since BioC 2.11 (R-2.15)
License Artistic-2.0
Depends GSEABase, limma(>= 3.15.14)
Imports Biobase, BiocGenerics, methods, GSEAlm, Category, Matrix (>= 1.0.9), parallel, annotate, genefilter, AnnotationDbi
Suggests DESeq, KEGG.db, reactome.db, RUnit, GO.db, mgsa
System Requirements
URL
Depends On Me gCMAPWeb
Imports Me
Suggests Me

Package Downloads

Package Source gCMAP_1.8.0.tar.gz
Windows Binary gCMAP_1.8.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) gCMAP_1.8.0.tgz
Mac OS X 10.9 (Mavericks)
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