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GeneAnswers (version 2.14.0)

Integrated Interpretation of Genes

Description

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

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Version

Version

2.14.0

License

LGPL (>= 2)

Maintainer

Lei Huang

Last Published

February 15th, 2017

Functions in GeneAnswers (2.14.0)

getCategoryTerms

Mapping Category IDs to Terms
geneAnnotationHeatmap

Make a concept-gene cross tabulation
geneAnswersSort

Sort enrichmentInfo of a GeneAnswers instance
getHomoGeneIDs

Get homologous genes of given genes
getPATHTerms

Get Pathway names of given KEGG IDs
getConceptTable

Generate top concepts-genes table
HsIALite

Human gene interaction matrix
entrez2caBIO

map Entrez gene IDs to caBIO gene IDs
getDOLiteTerms

Get DOLite Terms of Given DOLite IDs
groupReport

Generate a multigroup Concepts-genes analysis report
geneAnswersHomoMapping

Mapping homogenes for a GeneAnswers instance
getREACTOMEPATHTerms

Get Pathway names of given REACTOME PATH_DB IDs
geneConceptNet

Generate Concept-gene network
topPATHGenes

Present top KEGG enrichment test information with genes
getPATHList

Retrieve KEGG categories containing given genes
mouseExpr

Example mouse expression data
GeneAnswers-class

Class GeneAnswers: contain and describe the relationship between given gene data and specified category
topcaBIO.PATHGenes

Present top CABIO.PATH enrichment test information with genes
drawTable

Concept-Gene Networking Plotting
geneAnswersConcepts

Concept-Gene Networking Plotting
caBIO2entrez

map caBIO gene IDs to Entrez gene IDs
getConnectedGraph

build and display a network for given IDs
DmIALite

Fly gene interaction matrix
getCategoryList

Retrieve categories containing given genes
geneAnswersReadable

Make GeneAnswers Instance readable
geneAnswersConceptNet

Concept-Gene Networking Plotting
topCategory

Present top enrichment test information
DOLiteTerm

Disease Ontology Annotation Vector
searchEntrez

Search specified information from Entrez site
categoryNet

Plot Category Links
getNextGOIDs

retrieve parents or children GO IDs for given GO IDs
getSymbols

Convert entrez gene IDs to gene symbols
getREACTOMEPATHList

Retrieve REACTOME path categories containing given genes
getSingleLayerGraphIDs

retrieve direct interacted nodes for given IDs and interaction Matrix
getcaBIOPATHList

Retrieve caBIO path categories containing given genes
chartPlots

Pie Chart and Bar Plots
sampleGroupsData

Example human expression data
getcaBIOPATHTerms

Get Pathway names of given REACTOME PATH_DB IDs
topGO

Present top GO enrichment test information
topGOGenes

Present top GO enrichment test information with genes
MmIALite

Mouse gene interaction matrix
DOLite

Disease Ontology Annotation List
getGOList

Get GO list of given genes
geneAnswersConceptRelation

Display a network related to given concepts for a GeneAnswers instance
topPATH

Present top KEGG enrichment test information
RnIALite

Rat gene interaction matrix
topREACTOME.PATHGenes

Present top REACTOME.PATH enrichment test information with genes
getMultiLayerGraphIDs

retrieve multilayer interacted nodes for given IDs and interaction Matrix
DO

Several data objects related with DO (Disease Ontology) and its mapping to genes
GeneAnswers-package

Integrated Interpretation of Genes
geneAnswersBuilder

Build an object of a GeneAnswers class
geneAnswersHeatmap

Generate Concept-Gene Tabulates
getListGIF

getListGIF
humanExpr

Example human expression data
humanGeneInput

Example human gene data
geneAnswersChartPlots

Make pie chart and bar plot
mouseGeneInput

Example mouse gene data
topCategoryGenes

Present top enrichment test information with genes
buildNet

build and display a network for given IDs and interaction Matrix
topDOLITEGenes

Present top DOLITE enrichment test information with genes
topcaBIO.PATH

Present top CABIO.PATH enrichment test information
getTotalGeneNumber

Obtain the total number of genes in the given annotation library
topDOLITE

Present top DOLITE enrichment test information
topREACTOME.PATH

Present top REACTOME.PATH enrichment test information