R Graphical Manual

Last data update: 2014.03.03

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RDAVIDWebService : An R Package for retrieving data from DAVID into R objects using Web Services API.

Package: RDAVIDWebService
Type: Package
Title: An R Package for retrieving data from DAVID into R objects using
Web Services API.
Version: 1.10.0
Date: 2014-04-15
Author: Cristobal Fresno and Elmer A. Fernandez
Maintainer: Cristobal Fresno <cfresno@bdmg.com.ar>
Description: Tools for retrieving data from the Database for
Annotation, Visualization and Integrated Discovery (DAVID)
using Web Services into R objects. This package offers the main
functionalities of DAVID website including: i) user friendly
connectivity to upload gene/background list/s, change
gene/background position, select current specie/s, select
annotations, etc. ii) Reports of the submitted Gene List,
Annotation Category Summary, Gene/Term Clusters, Functional
Annotation Chart, Functional Annotation Table
License: GPL (>=2)
URL: http://www.bdmg.com.ar
Imports: Category, GO.db, RBGL, rJava
Depends: R (>= 2.14.1), methods, graph, GOstats, ggplot2
Collate: 'DAVIDdemo-ids.R' 'DAVIDdemo-geneList.R'
'DAVIDdemo-annotationSummary.R'
'DAVIDdemo-functionalAnnotationChart.R'
'DAVIDdemo-annotationTable.R' 'DAVIDdemo-clusterReport.R'
'DAVIDResult-class.R' 'DAVIDGenes-class.R'
'DAVIDFunctionalAnnotationChart-class.R' 'DAVIDCluster-class.R'
'DAVIDGeneCluster-class.R' 'DAVIDTermCluster-class.R'
'DAVIDFunctionalAnnotationTable-class.R' 'DAVIDGODag-class.R'
'DAVIDWebService-class.R' 'DAVIDClasses-show.R'
'DAVIDClasses-ids.R' 'DAVIDClasses-plot2D.R'
'DAVIDClasses-summary.R' 'DAVIDClasses-genes.R'
'DAVIDClasses-categories.R' 'DAVIDResult-getters.R'
'DAVIDGenes-methods.R' 'DAVIDCluster-methods.R'
'DAVIDFunctionalAnnotationTable-methods.R'
'DAVIDGODag-methods.R' 'DAVIDWebService-accessors.R'
'DAVIDWebService-methods.R' 'DAVIDWebService-reports.R'
'DAVIDClasses-constructor.R' 'RDAVIDWebService-package.R'
Suggests: Rgraphviz
InstallableEverywhere: yes
biocViews: Visualization, DifferentialExpression, GraphAndNetwork
NeedsCompilation: no
Packaged: 2016-05-04 05:00:02 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: DifferentialExpression, GraphAndNetwork, Visualization
● 6 images, 25 functions, 6 datasets
● Reverse Depends: 1

MineICA : Analysis of an ICA decomposition obtained on genomics data

Package: MineICA
Type: Package
Title: Analysis of an ICA decomposition obtained on genomics data
Version: 1.12.0
Date: 2012-03-16
Author: Anne Biton
Maintainer: Anne Biton <anne.biton@gmail.com>
Description: The goal of MineICA is to perform Independent Component
Analysis (ICA) on multiple transcriptome datasets, integrating
additional data (e.g molecular, clinical and pathological).
This Integrative ICA helps the biological interpretation of the
components by studying their association with variables (e.g
sample annotations) and gene sets, and enables the comparison
of components from different datasets using correlation-based
graph.
License: GPL-2
LazyLoad: yes
Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr,
ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats,
cluster, marray, mclust, RColorBrewer, colorspace, igraph,
Rgraphviz, graph, annotate, Hmisc, fastICA, JADE
Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db
Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph,
breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP,
breastCancerVDX
Enhances: doMC
Collate: 'AllClasses.R' 'AllGeneric.R' 'methods-IcaSet.R'
'methods-MineICAParams.R' 'compareAnalysis.R'
'functions_comp2annot.R' 'functions_comp2annottests.R'
'functions_enrich.R' 'functions.R' 'heatmap.plus.R'
'heatmapsOnSel.R' 'runAn.R' 'compareGenes.R'
biocViews: Visualization, MultipleComparison
NeedsCompilation: no
Packaged: 2016-05-05 03:47:04 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: MultipleComparison, Visualization
● 7 images, 66 functions, 7 datasets
● Reverse Depends: 0