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.

AuthorLei Huang, Gang Feng, Pan Du, Tian Xia, Xishu Wang, Jing, Wen, Warren Kibbe and Simon Lin
Date of publicationNone
MaintainerLei Huang <lhuang7@uchicago.edu> and Gang Feng <gilbertfeng@gmail.com>
LicenseLGPL (>= 2)
Version2.16.0

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...

Files in this package

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

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