GeneAnswers: Integrated Interpretation of Genes

GeneAnswers provides an integrated tool for biological or medical interpretation of the given one or more groups of genes by means of statistical test.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GeneAnswers")
AuthorLei Huang, Gang Feng, Pan Du, Tian Xia, Xishu Wang, Jing, Wen, Warren Kibbe and Simon Lin
Bioconductor views DataRepresentation GraphsAndNetworks Infrastructure Visualization
Date of publicationNone
MaintainerLei Huang <lhuang7@uchicago.edu> and Gang Feng <gilbertfeng@gmail.com>
LicenseLGPL (>= 2)
Version2.18.0

View on Bioconductor

Man pages

buildNet: build and display a network for given IDs and interaction...

caBIO2entrez: map caBIO gene IDs to Entrez gene IDs

caBIO.PATHGenes: Present top CABIO.PATH enrichment test information with genes

categoryNet: Plot Category Links

chartPlots: Pie Chart and Bar Plots

DmIALite: Fly gene interaction matrix

DO: Several data objects related with DO (Disease Ontology) and...

DOLite: Disease Ontology Annotation List

DOLiteTerm: Disease Ontology Annotation Vector

drawTable: Concept-Gene Networking Plotting

entrez2caBIO: map Entrez gene IDs to caBIO gene IDs

geneAnnotationHeatmap: Make a concept-gene cross tabulation

geneAnswersBuilder: Build an object of a GeneAnswers class

geneAnswersChartPlots: Make pie chart and bar plot

GeneAnswers-class: Class GeneAnswers: contain and describe the relationship...

geneAnswersConceptNet: Concept-Gene Networking Plotting

geneAnswersConceptRelation: Display a network related to given concepts for a GeneAnswers...

geneAnswersConcepts: Concept-Gene Networking Plotting

geneAnswersHeatmap: Generate Concept-Gene Tabulates

geneAnswersHomoMapping: Mapping homogenes for a GeneAnswers instance

GeneAnswers-package: Integrated Interpretation of Genes

geneAnswersReadable: Make GeneAnswers Instance readable

geneAnswersSort: Sort enrichmentInfo of a GeneAnswers instance

geneConceptNet: Generate Concept-gene network

getcaBIOPATHList: Retrieve caBIO path categories containing given genes

getcaBIOPATHTerms: Get Pathway names of given REACTOME PATH_DB IDs

getCategoryList: Retrieve categories containing given genes

getCategoryTerms: Mapping Category IDs to Terms

getConceptTable: Generate top concepts-genes table

getConnectedGraph: build and display a network for given IDs

getDOLiteTerms: Get DOLite Terms of Given DOLite IDs

getGOList: Get GO list of given genes

getHomoGeneIDs: Get homologous genes of given genes

getListGIF: getListGIF

getMultiLayerGraphIDs: retrieve multilayer interacted nodes for given IDs and...

getNextGOIDs: retrieve parents or children GO IDs for given GO IDs

getPATHList: Retrieve KEGG categories containing given genes

getPATHTerms: Get Pathway names of given KEGG IDs

getREACTOMEPATHList: Retrieve REACTOME path categories containing given genes

getREACTOMEPATHTerms: Get Pathway names of given REACTOME PATH_DB IDs

getSingleLayerGraphIDs: retrieve direct interacted nodes for given IDs and...

getSymbols: Convert entrez gene IDs to gene symbols

getTotalGeneNumber: Obtain the total number of genes in the given annotation...

groupReport: Generate a multigroup Concepts-genes analysis report

HsIALite: Human gene interaction matrix

humanExpr: Example human expression data

humanGeneInput: Example human gene data

MmIALite: Mouse gene interaction matrix

mouseExpr: Example mouse expression data

mouseGeneInput: Example mouse gene data

RnIALite: Rat gene interaction matrix

sampleGroupsData: Example human expression data

searchEntrez: Search specified information from Entrez site

topcaBIO.PATH: Present top CABIO.PATH enrichment test information

topCategory: Present top enrichment test information

topCategoryGenes: Present top enrichment test information with genes

topDOLITE: Present top DOLITE enrichment test information

topDOLITEGenes: Present top DOLITE enrichment test information with genes

topGO: Present top GO enrichment test information

topGOGenes: Present top GO enrichment test information with genes

topPATH: Present top KEGG enrichment test information

topPATHGenes: Present top KEGG enrichment test information with genes

topREACTOME.PATH: Present top REACTOME.PATH enrichment test information

topREACTOME.PATHGenes: Present top REACTOME.PATH enrichment test information with...

Functions

buildNet Man page
caBIO2entrez Man page
categoryNet Man page
chartPlots Man page
class:GeneAnswers Man page
DmIALite Man page
DO Man page
DO2gene.map Man page
DO.graph.closure.gene Man page
DO.graph.gene Man page
DOLite Man page
DOLiteTerm Man page
DO.terms Man page
drawTable Man page
entrez2caBIO Man page
gene2DO.map Man page
geneAnnotationHeatmap Man page
GeneAnswers Man page
geneAnswersBuilder Man page
geneAnswersChartPlots Man page
GeneAnswers-class Man page
geneAnswersConceptNet Man page
geneAnswersConceptRelation Man page
geneAnswersConcepts Man page
geneAnswersHeatmap Man page
geneAnswersHomoMapping Man page
GeneAnswers-package Man page
geneAnswersReadable Man page
geneAnswersSort Man page
geneConceptNet Man page
getAnnLib Man page
getAnnLib,GeneAnswers-method Man page
getcaBIOPATHList Man page
getcaBIOPATHTerms Man page
getCategoryList Man page
getCategoryTerms Man page
getCategoryType Man page
getCategoryType,GeneAnswers-method Man page
getConceptTable Man page
getConnectedGraph Man page
getDOLiteTerms Man page
getEnrichmentInfo Man page
getEnrichmentInfo,GeneAnswers-method Man page
getGeneExprProfile Man page
getGeneExprProfile,GeneAnswers-method Man page
getGeneInput Man page
getGeneInput,GeneAnswers-method Man page
getGenesInCategory Man page
getGenesInCategory,GeneAnswers-method Man page
getGOList Man page
getHomoGeneIDs Man page
getListGIF Man page
getMultiLayerGraphIDs Man page
getNextGOIDs Man page
getPATHList Man page
getPATHTerms Man page
getPValueT Man page
getPValueT,GeneAnswers-method Man page
getREACTOMEPATHList Man page
getREACTOMEPATHTerms Man page
getSingleLayerGraphIDs Man page
getSymbols Man page
getTestType Man page
getTestType,GeneAnswers-method Man page
getTotalGeneNumber Man page
groupReport Man page
HsIALite Man page
humanExpr Man page
humanGeneInput Man page
MmIALite Man page
mouseExpr Man page
mouseGeneInput Man page
RnIALite Man page
sampleGroupsData Man page
searchEntrez Man page
setAnnLib Man page
setAnnLib,GeneAnswers-method Man page
setCategoryType Man page
setCategoryType,GeneAnswers-method Man page
setEnrichmentInfo Man page
setEnrichmentInfo,GeneAnswers-method Man page
setGeneExprProfile Man page
setGeneExprProfile,GeneAnswers-method Man page
setGeneInput Man page
setGeneInput,GeneAnswers-method Man page
setGenesInCategory Man page
setGenesInCategory,GeneAnswers-method Man page
setPValueT Man page
setPValueT,GeneAnswers-method Man page
setTestType Man page
setTestType,GeneAnswers-method Man page
show Man page
show,GeneAnswers-method Man page
summary Man page
summary,GeneAnswers-method Man page
topcaBIO.PATH Man page
topcaBIO.PATHGenes Man page
topCategory Man page
topCategoryGenes Man page
topDOLITE Man page
topDOLITEGenes Man page
topGO Man page
topGOGenes Man page
topPATH Man page
topPATHGenes Man page
topREACTOME.PATH Man page
topREACTOME.PATHGenes Man page

Files

DESCRIPTION
NAMESPACE
R
R/GeneAnswersClass.R R/buildNet.R R/caBIO2entrez.R R/categoryNet.R R/chartPlots.R R/drawTable.R R/entrez2caBIO.R R/geneAnnotationHeatmap.R R/geneAnswersBuilder.R R/geneAnswersChartPlots.R R/geneAnswersConceptNet.R R/geneAnswersConceptRelation.R R/geneAnswersConcepts.R R/geneAnswersHeatmap.R R/geneAnswersHomoMapping.R R/geneAnswersReadable.R R/geneAnswersSort.R R/geneConceptNet.R R/getCategoryList.R R/getCategoryTerms.R R/getConceptTable.R R/getConnectedGraph.R R/getDOLiteTerms.R R/getGOList.R R/getHomoGeneIDs.R R/getListGIF.R R/getMultiLayerGraphIDs.R R/getNextGOIDs.R R/getPATHList.R R/getPATHTerms.R R/getREACTOMEPATHList.R R/getREACTOMEPATHTerms.R R/getSingleLayerGraphIDs.R R/getSymbols.R R/getTotalGeneNumber.R R/getcaBIOPATHList.R R/getcaBIOPATHTerms.R R/groupReport.R R/searchEntrez.R R/topCategory.R R/topCategoryGenes.R R/topDOLITE.R R/topDOLITEGenes.R R/topGO.R R/topGOGenes.R R/topPATH.R R/topPATHGenes.R R/topREACTOME.PATH.R R/topREACTOME.PATHGenes.R R/topcaBIO.PATH.R R/topcaBIO.PATHGenes.R R/zzz.R
build
build/vignette.rds
data
data/DO.rda
data/DOLite.rda
data/DOLiteTerm.rda
data/DmIALite.rda
data/HsIALite.rda
data/MmIALite.rda
data/RnIALite.rda
data/datalist
data/humanExpr.rda
data/humanGeneInput.rda
data/mouseExpr.rda
data/mouseGeneInput.rda
data/sampleGroupsData.rda
inst
inst/External
inst/External/NetworkTransformer.jar
inst/External/js
inst/External/js/cytoscape_web
inst/External/js/cytoscape_web/AC_OETags.min.js
inst/External/js/cytoscape_web/cytoscapeweb.min.js
inst/External/js/cytoscape_web/json2.min.js
inst/External/js/src
inst/External/js/src/AC_OETags.js
inst/External/js/src/cytoscapeweb.js
inst/External/js/src/json2.js
inst/External/swf
inst/External/swf/CytoscapeWeb.swf
inst/External/swf/playerProductInstall.swf
inst/NEWS
inst/doc
inst/doc/geneAnswers.R
inst/doc/geneAnswers.Rnw
inst/doc/geneAnswers.pdf
inst/doc/getListGIF.R
inst/doc/getListGIF.Rnw
inst/doc/getListGIF.pdf
man
man/DO.Rd man/DOLite.Rd man/DOLiteTerm.Rd man/DmIALite.Rd man/GeneAnswers-class.Rd man/GeneAnswers-package.Rd man/HsIALite.Rd man/MmIALite.Rd man/RnIALite.Rd man/buildNet.Rd man/caBIO.PATHGenes.Rd man/caBIO2entrez.Rd man/categoryNet.Rd man/chartPlots.Rd man/drawTable.Rd man/entrez2caBIO.Rd man/geneAnnotationHeatmap.Rd man/geneAnswersBuilder.Rd man/geneAnswersChartPlots.Rd man/geneAnswersConceptNet.Rd man/geneAnswersConceptRelation.Rd man/geneAnswersConcepts.Rd man/geneAnswersHeatmap.Rd man/geneAnswersHomoMapping.Rd man/geneAnswersReadable.Rd man/geneAnswersSort.Rd man/geneConceptNet.Rd man/getCategoryList.Rd man/getCategoryTerms.Rd man/getConceptTable.Rd man/getConnectedGraph.Rd man/getDOLiteTerms.Rd man/getGOList.Rd man/getHomoGeneIDs.Rd man/getListGIF.Rd man/getMultiLayerGraphIDs.Rd man/getNextGOIDs.Rd man/getPATHList.Rd man/getPATHTerms.Rd man/getREACTOMEPATHList.Rd man/getREACTOMEPATHTerms.Rd man/getSingleLayerGraphIDs.Rd man/getSymbols.Rd man/getTotalGeneNumber.Rd man/getcaBIOPATHList.Rd man/getcaBIOPATHTerms.Rd man/groupReport.Rd man/humanExpr.Rd man/humanGeneInput.Rd man/mouseExpr.Rd man/mouseGeneInput.Rd man/sampleGroupsData.Rd man/searchEntrez.Rd man/topCategory.Rd man/topCategoryGenes.Rd man/topDOLITE.Rd man/topDOLITEGenes.Rd man/topGO.Rd man/topGOGenes.Rd man/topPATH.Rd man/topPATHGenes.Rd man/topREACTOME.PATH.Rd man/topREACTOME.PATHGenes.Rd man/topcaBIO.PATH.Rd
vignettes
vignettes/barplot01.jpg
vignettes/concept01.jpg
vignettes/conceptNet01.jpg
vignettes/conceptNet01a.jpg
vignettes/conceptNet02.jpg
vignettes/conceptNet03.jpg
vignettes/conceptNet04.jpg
vignettes/conceptNet05.jpg
vignettes/conceptNet06.jpg
vignettes/conceptNet07.jpg
vignettes/flowChart_summarization.png
vignettes/flowchart.jpg
vignettes/flowchart.png
vignettes/geneAnswers.Rnw
vignettes/geneInteraction01.jpg
vignettes/geneInteraction02.jpg
vignettes/geneInteraction03.jpg
vignettes/geneInteraction04.jpg
vignettes/getListGIF.Rnw
vignettes/gostrt.jpg
vignettes/multi.jpg
vignettes/nodeAttrFileFormat.png
vignettes/piechart01.jpg
vignettes/tmp.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.