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GeneAnswers (version 2.12.0)

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

2.12.0

License

LGPL (>= 2)

Maintainer

Lei Huang

Last Published

February 15th, 2017

Functions in GeneAnswers (2.12.0)

Pie Chart and Bar Plots

Fly gene interaction matrix

geneAnswersHeatmap

Generate Concept-Gene Tabulates

getcaBIOPATHList

Retrieve caBIO path categories containing given genes

geneAnswersConcepts

Concept-Gene Networking Plotting

getcaBIOPATHTerms

Get Pathway names of given REACTOME PATH_DB IDs

Get homologous genes of given genes

topCategoryGenes

Present top enrichment test information with genes

Generate a multigroup Concepts-genes analysis report

getTotalGeneNumber

Obtain the total number of genes in the given annotation library

Present top enrichment test information

Disease Ontology Annotation Vector

GeneAnswers-class

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

Concept-Gene Networking Plotting

GeneAnswers-package

Integrated Interpretation of Genes

getCategoryList

Retrieve categories containing given genes

getCategoryTerms

Mapping Category IDs to Terms

Retrieve KEGG categories containing given genes

Get Pathway names of given KEGG IDs

Example mouse expression data

Example mouse gene data

geneAnswersBuilder

Build an object of a GeneAnswers class

geneAnswersHomoMapping

Mapping homogenes for a GeneAnswers instance

geneAnswersChartPlots

Make pie chart and bar plot

geneAnswersReadable

Make GeneAnswers Instance readable

getMultiLayerGraphIDs

retrieve multilayer interacted nodes for given IDs and interaction Matrix

retrieve parents or children GO IDs for given GO IDs

Rat gene interaction matrix

sampleGroupsData

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

getConnectedGraph

build and display a network for given IDs

geneAnnotationHeatmap

Make a concept-gene cross tabulation

getREACTOMEPATHList

Retrieve REACTOME path categories containing given genes

getConceptTable

Generate top concepts-genes table

getREACTOMEPATHTerms

Get Pathway names of given REACTOME PATH_DB IDs

getSingleLayerGraphIDs

retrieve direct interacted nodes for given IDs and interaction Matrix

Convert entrez gene IDs to gene symbols

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

Human gene interaction matrix

Disease Ontology Annotation List

Present top GO enrichment test information

Example human expression data

Present top GO enrichment test information with genes

Present top KEGG enrichment test information

Present top KEGG enrichment test information with genes

Present top DOLITE enrichment test information

Present top DOLITE enrichment test information with genes

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

geneAnswersConceptRelation

Display a network related to given concepts for a GeneAnswers instance

geneAnswersConceptNet

Concept-Gene Networking Plotting

Plot Category Links

Generate Concept-gene network

geneAnswersSort

Sort enrichmentInfo of a GeneAnswers instance

Get GO list of given genes

Example human gene data

Get DOLite Terms of Given DOLite IDs

Search specified information from Entrez site

Mouse gene interaction matrix

Present top CABIO.PATH enrichment test information