Learn R Programming
⚠️There's a newer version (2.14.0) of this package.Take me there.

GeneAnswers (version 2.8.0)

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.

Copy Link

Version

Version

2.8.0

License

LGPL (>= 2)

Maintainer

Lei Huang

Last Published

February 15th, 2017

Functions in GeneAnswers (2.8.0)

DOLite

Disease Ontology Annotation List
geneAnswersSort

Sort enrichmentInfo of a GeneAnswers instance
DO

Several data objects related with DO (Disease Ontology) and its mapping to genes
geneConceptNet

Generate Concept-gene network
getPATHList

Retrieve KEGG categories containing given genes
getPATHTerms

Get Pathway names of given KEGG IDs
getSingleLayerGraphIDs

retrieve direct interacted nodes for given IDs and interaction Matrix
getSymbols

Convert entrez gene IDs to gene symbols
topDOLITE

Present top DOLITE enrichment test information
topDOLITEGenes

Present top DOLITE enrichment test information with genes
topcaBIO.PATHGenes

Present top CABIO.PATH enrichment test information with genes
buildNet

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

Make pie chart and bar plot
geneAnswersBuilder

Build an object of a GeneAnswers class
getMultiLayerGraphIDs

retrieve multilayer interacted nodes for given IDs and interaction Matrix
getNextGOIDs

retrieve parents or children GO IDs for given GO IDs
drawTable

Concept-Gene Networking Plotting
DOLiteTerm

Disease Ontology Annotation Vector
topREACTOME.PATH

Present top REACTOME.PATH enrichment test information
topREACTOME.PATHGenes

Present top REACTOME.PATH enrichment test information with genes
geneAnswersConcepts

Concept-Gene Networking Plotting
geneAnswersHeatmap

Generate Concept-Gene Tabulates
getcaBIOPATHList

Retrieve caBIO path categories containing given genes
getcaBIOPATHTerms

Get Pathway names of given REACTOME PATH_DB IDs
getListGIF

getListGIF
getHomoGeneIDs

Get homologous genes of given genes
caBIO2entrez

map caBIO gene IDs to Entrez gene IDs
categoryNet

Plot Category Links
entrez2caBIO

map Entrez gene IDs to caBIO gene IDs
geneAnnotationHeatmap

Make a concept-gene cross tabulation
getCategoryList

Retrieve categories containing given genes
getCategoryTerms

Mapping Category IDs to Terms
getDOLiteTerms

Get DOLite Terms of Given DOLite IDs
getGOList

Get GO list of given genes
humanGeneInput

Example human gene data
MmIALite

Mouse gene interaction matrix
searchEntrez

Search specified information from Entrez site
topcaBIO.PATH

Present top CABIO.PATH enrichment test information
mouseExpr

Example mouse expression data
mouseGeneInput

Example mouse gene data
topGO

Present top GO enrichment test information
topGOGenes

Present top GO enrichment test information with genes
chartPlots

Pie Chart and Bar Plots
DmIALite

Fly gene interaction matrix
getConceptTable

Generate top concepts-genes table
geneAnswersConceptNet

Concept-Gene Networking Plotting
geneAnswersConceptRelation

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

build and display a network for given IDs
HsIALite

Human gene interaction matrix
humanExpr

Example human expression data
RnIALite

Rat gene interaction matrix
GeneAnswers-class

Class GeneAnswers: contain and describe the relationship between given gene data and specified category
GeneAnswers-package

Integrated Interpretation of Genes
sampleGroupsData

Example human expression data
topPATH

Present top KEGG enrichment test information
topPATHGenes

Present top KEGG enrichment test information with genes
geneAnswersHomoMapping

Mapping homogenes for a GeneAnswers instance
geneAnswersReadable

Make GeneAnswers Instance readable
getREACTOMEPATHList

Retrieve REACTOME path categories containing given genes
getREACTOMEPATHTerms

Get Pathway names of given REACTOME PATH_DB IDs
groupReport

Generate a multigroup Concepts-genes analysis report
topCategory

Present top enrichment test information
getTotalGeneNumber

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

Present top enrichment test information with genes