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GeneAnswers (version 2.10.0)

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

2.10.0

License

LGPL (>= 2)

Maintainer

Lei Huang

Last Published

February 15th, 2017

Functions in GeneAnswers (2.10.0)

Disease Ontology Annotation Vector

geneAnswersConceptRelation

Display a network related to given concepts for a GeneAnswers instance

geneAnswersConceptNet

Concept-Gene Networking Plotting

geneAnswersSort

Sort enrichmentInfo of a GeneAnswers instance

Human gene interaction matrix

Generate Concept-gene network

Example human expression data

topcaBIO.PATHGenes

Present top CABIO.PATH enrichment test information with genes

build and display a network for given IDs and interaction Matrix

map Entrez gene IDs to caBIO gene IDs

geneAnnotationHeatmap

Make a concept-gene cross tabulation

Concept-Gene Networking Plotting

topREACTOME.PATH

Present top REACTOME.PATH enrichment test information

topREACTOME.PATHGenes

Present top REACTOME.PATH enrichment test information with genes

map caBIO gene IDs to Entrez gene IDs

Plot Category Links

geneAnswersConcepts

Concept-Gene Networking Plotting

geneAnswersHeatmap

Generate Concept-Gene Tabulates

getCategoryList

Retrieve categories containing given genes

getConceptTable

Generate top concepts-genes table

getConnectedGraph

build and display a network for given IDs

Get GO list of given genes

Get DOLite Terms of Given DOLite IDs

Generate a multigroup Concepts-genes analysis report

getTotalGeneNumber

Obtain the total number of genes in the given annotation library

getCategoryTerms

Mapping Category IDs to Terms

Retrieve KEGG categories containing given genes

Get Pathway names of given KEGG IDs

getSingleLayerGraphIDs

retrieve direct interacted nodes for given IDs and interaction Matrix

Present top DOLITE enrichment test information with genes

Convert entrez gene IDs to gene symbols

Present top DOLITE enrichment test information

Search specified information from Entrez site

Present top KEGG enrichment test information

Present top CABIO.PATH enrichment test information

Present top KEGG enrichment test information with genes

geneAnswersBuilder

Build an object of a GeneAnswers class

getcaBIOPATHList

Retrieve caBIO path categories containing given genes

geneAnswersChartPlots

Make pie chart and bar plot

getREACTOMEPATHList

Retrieve REACTOME path categories containing given genes

getcaBIOPATHTerms

Get Pathway names of given REACTOME PATH_DB IDs

getREACTOMEPATHTerms

Get Pathway names of given REACTOME PATH_DB IDs

Present top GO enrichment test information with genes

Present top GO enrichment test information

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

Disease Ontology Annotation List

GeneAnswers-class

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

GeneAnswers-package

Integrated Interpretation of Genes

geneAnswersHomoMapping

Mapping homogenes for a GeneAnswers instance

Get homologous genes of given genes

Example mouse expression data

Present top enrichment test information

Example mouse gene data

geneAnswersReadable

Make GeneAnswers Instance readable

topCategoryGenes

Present top enrichment test information with genes

Pie Chart and Bar Plots

Fly gene interaction matrix

getMultiLayerGraphIDs

retrieve multilayer interacted nodes for given IDs and interaction Matrix

retrieve parents or children GO IDs for given GO IDs

Mouse gene interaction matrix

Example human gene data

Rat gene interaction matrix

sampleGroupsData

Example human expression data