Package: cogena
Version: 1.0.0
Title: co-expressed gene-set enrichment analysis
Authors@R: c(person("Zhilong", "Jia", role =c("aut", "cre"),
        email="zhilongjia@gmail.com"), person("Michael", "Barnes", role
        = "aut", email="m.r.barnes@qmul.ac.uk"))
Description: Description: Gene set enrichment analysis is a valuable
        tool for the study of molecular mechanisms that underpin
        complex biological traits. As the method is conventionally used
        on entire omic datasets, such as transcriptomes, it may be
        dominated by pathways and processes that are substantially
        represented in a dataset, however the approach may overlook
        smaller scale, but highly correlated cellular events that may
        be of great biological relevance. In order to detect these
        discrete molecular triggers, we developed a tool, co-expressed
        gene-set enrichment analysis (cogena), for clustering
        differentially expressed genes and identification of highly
        correlated molecular expression clusters. Cogena offers the
        user a range of clustering methods, including hierarchical
        clustering, model based clustering and self-organised mapping,
        based on different distance metrics like correlation and mutual
        information. After obtaining and visualising clusters, cogena
        performs gene set enrichment. These gene sets can be sourced
        from the Molecular Signatures Database (MSigDB) or user-defined
        gene sets. By performing gene set enrichment across expression
        clusters, we find considerable enhancement in the resolution of
        molecular signatures in omic data at the cluster level compared
        to the whole.
biocViews: Clustering, GeneSetEnrichment, GeneExpression,
        Visualization, Pathways, Microarray, Sequencing,
        SystemsBiology, DataRepresentation, DataImport
Depends: R (>= 3.2), cluster, ggplot2, gplots, amap
Imports: methods, class, foreach, parallel, doParallel, fastcluster,
        corrplot, reshape2, devtools
Suggests: Biobase, annotate, kohonen, mclust, biwt, knitr
Collate: dist_class.R cogena_class.R PD.R PEI.R cogena.R
        cogena_methods.R enrichment.R gene2set.R geneInCluster.R
        geneExpInCluster.R corInCluster.R gmt2list.R heatmap.3.R
        heatmapCluster.R heatmapPEI.R heatmapPEI2.R hubgeneInCluster.R
        optCluster.R sota.R vClusters.R
License: LGPL-3
LazyData: true
Encoding: UTF-8
URL: https://github.com/zhilongjia/cogena
NeedsCompilation: no
BugReports: https://github.com/zhilongjia/cogena/issues
VignetteBuilder: knitr
Author: Zhilong Jia [aut, cre], Michael Barnes [aut]
Maintainer: Zhilong Jia <zhilongjia@gmail.com>
Packaged: 2015-04-17 05:56:35 UTC; biocbuild
Built: R 3.2.0; ; 2015-04-17 07:40:23 UTC; windows
