R Graphical Manual

Last data update: 2014.03.03

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EGSEA : Ensemble of Gene Set Enrichment Analyses

Package: EGSEA
Title: Ensemble of Gene Set Enrichment Analyses
Version: 1.0.3
Date: 10-05-2016
Author: Monther Alhamdoosh, Milica Ng and Matthew Ritchie
Maintainer: Monther Alhamdoosh <m.hamdoosh@gmail.com>
Description: This package implements the Ensemble of Gene Set Enrichment
Analyses (EGSEA) method for gene set testing.
biocViews: DifferentialExpression, GO, GeneExpression,
GeneSetEnrichment, Genetics, Microarray, MultipleComparison,
OneChannel, Pathways, RNASeq, Sequencing, Software,
SystemsBiology, TwoChannel,Metabolomics, Proteomics, KEGG,
GraphAndNetwork
Depends: R (>= 3.3), Biobase, gage (>= 2.14.4), AnnotationDbi, topGO
(>= 2.16.0), pathview (>= 1.4.2)
Imports: PADOG (>= 1.6.0), GSVA (>= 1.12.0), globaltest (>= 5.18.0),
limma (>= 3.20.9), edgeR (>= 3.6.8), HTMLUtils (>= 0.1.5),
hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0),
safe (>= 3.4.0), stringi (>= 0.5.0), parallel, stats,
grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db,
org.Rn.eg.db, EGSEAdata
License: GPL-2
LazyLoad: yes
NeedsCompilation: no
Suggests: BiocStyle, knitr, testthat
VignetteBuilder: knitr
RoxygenNote: 5.0.1
Packaged: 2016-05-16 06:17:00 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, Genetics, GraphAndNetwork, KEGG, Metabolomics, Microarray, MultipleComparison, OneChannel, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, TwoChannel
● 0 images, 13 functions, 0 datasets
● Reverse Depends: 0

EnrichmentBrowser : Seamless navigation through combined results of set-based and network-based enrichment analysis

Package: EnrichmentBrowser
Version: 2.2.2
Date: 2016-05-19
Title: Seamless navigation through combined results of set-based and
network-based enrichment analysis
Author: Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
Maintainer: Ludwig Geistlinger <Ludwig.Geistlinger@bio.ifi.lmu.de>
Depends: R (>= 3.0.0), Biobase, GSEABase, pathview
Imports: AnnotationDbi, ComplexHeatmap, DESeq2, EDASeq, GO.db,
KEGGREST, KEGGgraph, MASS, ReportingTools, Rgraphviz,
S4Vectors, SPIA, SummarizedExperiment, biocGraph, edgeR,
geneplotter, graph, hwriter, limma, safe, topGO
Suggests: ALL, BiocStyle, airway, hgu95av2.db
Description: The EnrichmentBrowser package implements essential functionality
for the enrichment analysis of gene expression data. The analysis combines
the advantages of set-based and network-based enrichment analysis in order
to derive high-confidence gene sets and biological pathways that are
differentially regulated in the expression data under investigation.
Besides, the package facilitates the visualization and exploration of such
sets and pathways.
License: Artistic-2.0
biocViews: Microarray, RNASeq, GeneExpression, DifferentialExpression,
Pathways, GraphAndNetwork, Network, GeneSetEnrichment,
NetworkEnrichment, Visualization, ReportWriting
NeedsCompilation: no
Packaged: 2016-05-20 04:51:09 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Visualization
● 5 images, 18 functions, 0 datasets
● Reverse Depends: 0