GeneAnswers: Integrated Interpretation of Genes

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

Author
Lei Huang, Gang Feng, Pan Du, Tian Xia, Xishu Wang, Jing, Wen, Warren Kibbe and Simon Lin
Date of publication
None
Maintainer
Lei Huang <lhuang7@uchicago.edu> and Gang Feng <gilbertfeng@gmail.com>
License
LGPL (>= 2)
Version
2.16.0

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