XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis
Version 1.1.1

The central goal of XGR is to provide a data interpretation system necessary to do "big data" science. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes, SNPs or genomic regions, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks, TF binding sites and genomic segments) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.

Browse man pages Browse package API and functions Browse package files

AuthorHai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Bioconductor views Bioinformatics
Date of publication2017-05-16 11:07:07
MaintainerHai Fang <hfang@well.ox.ac.uk>
LicenseGPL-2
Version1.1.1
URL http://XGR.r-forge.r-project.org http://galahad.well.ox.ac.uk/XGR http://rpubs.com/hfang/XGR
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("XGR", repos="http://R-Forge.R-project.org")

Man pages

eTerm: Definition for S3 class 'eTerm'
ImmunoBase: Immune-disease associated variants, regions and genes from...
JKscience_TS2A: Table S2A for cis-eQTLs among shared datasets from Benjamin...
xCheckParallel: Function to check whether parallel computing should be used...
xCircos: Function to visualise a network as a circos plot
xColormap: Function to define a colormap
xConverter: Function to convert an object between graph classes
xDAGanno: Function to generate a subgraph of a direct acyclic graph...
xDAGpropagate: Function to generate a subgraph of a direct acyclic graph...
xDAGsim: Function to calculate pair-wise semantic similarity between...
xDefineNet: Function to define a gene network
xEnrichBarplot: Function to visualise enrichment results using a barplot
xEnrichCompare: Function to compare enrichment results using side-by-side...
xEnrichConciser: Function to make enrichment results conciser by removing...
xEnrichDAGplot: Function to visualise enrichment results using a direct...
xEnrichDAGplotAdv: Function to visualise comparative enrichment results using a...
xEnricher: Function to conduct enrichment analysis given the input data...
xEnricherGenes: Function to conduct enrichment analysis given a list of genes...
xEnricherSNPs: Function to conduct enrichment analysis given a list of SNPs...
xEnricherYours: Function to conduct enrichment analysis given YOUR own input...
xEnrichNetplot: Function to visualise enrichment results using different...
xEnrichViewer: Function to view enrichment results
xFunArgs: Function to assign (and evaluate) arguments with default...
xGR: Function to create a GRanges object given a list of genomic...
xGR2GeneScores: Function to identify likely modulated seed genes given a list...
xGR2nGenes: Function to define nearby genes given a list of genomic...
xGRsampling: Function to generate random samples for data genomic regions...
xGRscores: Function to score genomic regions based on the given...
xGRviaGeneAnno: Function to conduct region-based enrichment analysis using...
xGRviaGenomicAnno: Function to conduct region-based enrichment analysis using...
xGRviaGenomicAnnoAdv: Function to conduct region-based enrichment analysis using...
xLiftOver: Function to lift genomic intervals from one genome build to...
xRd2HTML: Function to convert Rd files to HTML files
xRDataLoader: Function to load the package built-in RData
xRdWrap: Function to wrap texts from Rd files
xSM2DF: Function to create a data frame (with three columns) from a...
xSNP2GeneScores: Function to identify likely modulated seed genes given a list...
xSNP2nGenes: Function to define nearby genes given a list of SNPs
xSNPlocations: Function to extract genomic locations given a list of SNPs
xSNPscores: Function to score lead or LD SNPs based on the given...
xSocialiser: Function to calculate pair-wise semantic similarity given the...
xSocialiserDAGplot: Function to draw DAG plot for visualising terms used to...
xSocialiserDAGplotAdv: Function to draw DAG plot for comparing two sets of terms...
xSocialiserGenes: Function to calculate pair-wise semantic similarity given a...
xSocialiserNetplot: Function to visualise terms used to annotate an input SNP or...
xSocialiserSNPs: Function to calculate pair-wise semantic similarity given a...
xSparseMatrix: Function to create a sparse matrix for an input file with...
xSubneterGenes: Function to identify a subnetwork from an input network and...
xSubneterGR: Function to identify a gene network from an input network...
xSubneterSNPs: Function to identify a gene network from an input network...
xSymbol2GeneID: Function to convert gene symbols to entrez geneid
xVisInterp: Function to visualise interpolated irregular data
xVisInterpAnimate: Function to animate the visualisation of interpolated...
xVisKernels: Function to visualise distance kernel functions
xVisNet: Function to visualise a graph object of class "igraph"

Functions

ImmunoBase Man page
JKscience_TS2A Man page
eTerm Man page Source code
print.eTerm Man page Source code
xCheckParallel Man page Source code
xCircos Man page Source code
xColormap Man page Source code
xConverter Man page Source code
xDAGanno Man page Source code
xDAGpropagate Man page Source code
xDAGsim Man page Source code
xDefineNet Man page Source code
xEnrichBarplot Man page Source code
xEnrichCompare Man page Source code
xEnrichConciser Man page Source code
xEnrichDAGplot Man page Source code
xEnrichDAGplotAdv Man page Source code
xEnrichNetplot Man page Source code
xEnrichViewer Man page Source code
xEnricher Man page Source code
xEnricherGenes Man page Source code
xEnricherSNPs Man page Source code
xEnricherYours Man page Source code
xFunArgs Man page Source code
xGR Man page Source code
xGR2GeneScores Man page Source code
xGR2nGenes Man page Source code
xGRsampling Man page Source code
xGRscores Man page Source code
xGRviaGeneAnno Man page Source code
xGRviaGenomicAnno Man page Source code
xGRviaGenomicAnnoAdv Man page Source code
xLiftOver Man page Source code
xRDataLoader Man page Source code
xRd2HTML Man page Source code
xRdWrap Man page Source code
xSM2DF Man page Source code
xSNP2GeneScores Man page Source code
xSNP2nGenes Man page Source code
xSNPlocations Man page Source code
xSNPscores Man page Source code
xSocialiser Man page Source code
xSocialiserDAGplot Man page Source code
xSocialiserDAGplotAdv Man page Source code
xSocialiserGenes Man page Source code
xSocialiserNetplot Man page Source code
xSocialiserSNPs Man page Source code
xSparseMatrix Man page Source code
xSubneterGR Man page Source code
xSubneterGenes Man page Source code
xSubneterSNPs Man page Source code
xSymbol2GeneID Man page Source code
xVisInterp Man page Source code
xVisInterpAnimate Man page Source code
xVisKernels Man page Source code
xVisNet Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/ClassMethod-XGR.r
R/xCheckParallel.r
R/xCircos.r
R/xColormap.r
R/xConverter.r
R/xDAGanno.r
R/xDAGpropagate.r
R/xDAGsim.r
R/xDefineNet.r
R/xEnrichBarplot.r
R/xEnrichCompare.r
R/xEnrichConciser.r
R/xEnrichDAGplot.r
R/xEnrichDAGplotAdv.r
R/xEnrichNetplot.r
R/xEnrichViewer.r
R/xEnricher.r
R/xEnricherGenes.r
R/xEnricherSNPs.r
R/xEnricherYours.r
R/xFunArgs.r
R/xGR.r
R/xGR2GeneScores.r
R/xGR2nGenes.r
R/xGRsampling.r
R/xGRscores.r
R/xGRviaGeneAnno.r
R/xGRviaGenomicAnno.r
R/xGRviaGenomicAnnoAdv.r
R/xLiftOver.r
R/xRDataLoader.r
R/xRd2HTML.r
R/xRdWrap.r
R/xSM2DF.r
R/xSNP2GeneScores.r
R/xSNP2nGenes.r
R/xSNPlocations.r
R/xSNPscores.r
R/xSocialiser.r
R/xSocialiserDAGplot.r
R/xSocialiserDAGplotAdv.r
R/xSocialiserGenes.r
R/xSocialiserNetplot.r
R/xSocialiserSNPs.r
R/xSparseMatrix.r
R/xSubneterGR.r
R/xSubneterGenes.r
R/xSubneterSNPs.r
R/xSymbol2GeneID.r
R/xVisInterp.r
R/xVisInterpAnimate.r
R/xVisKernels.r
R/xVisNet.r
data
data/ImmunoBase.RData
data/JKscience_TS2A.RData
inst
inst/CITATION
inst/ImmunoBase.html
inst/JKscience_TS2A.html
inst/NEWS
inst/XGR.icon.png
inst/XGR.logo.png
inst/eTerm.html
inst/xCheckParallel.html
inst/xCircos.html
inst/xColormap.html
inst/xConverter.html
inst/xDAGanno.html
inst/xDAGpropagate.html
inst/xDAGsim.html
inst/xDefineNet.html
inst/xEnrichBarplot.html
inst/xEnrichCompare.html
inst/xEnrichConciser.html
inst/xEnrichDAGplot.html
inst/xEnrichDAGplotAdv.html
inst/xEnrichNetplot.html
inst/xEnrichViewer.html
inst/xEnricher.html
inst/xEnricherGenes.html
inst/xEnricherSNPs.html
inst/xEnricherYours.html
inst/xFunArgs.html
inst/xGR.html
inst/xGR2GeneScores.html
inst/xGR2nGenes.html
inst/xGRsampling.html
inst/xGRscores.html
inst/xGRviaGeneAnno.html
inst/xGRviaGenomicAnno.html
inst/xGRviaGenomicAnnoAdv.html
inst/xLiftOver.html
inst/xRDataLoader.html
inst/xRd2HTML.html
inst/xRdWrap.html
inst/xSM2DF.html
inst/xSNP2GeneScores.html
inst/xSNP2nGenes.html
inst/xSNPlocations.html
inst/xSNPscores.html
inst/xSocialiser.html
inst/xSocialiserDAGplot.html
inst/xSocialiserDAGplotAdv.html
inst/xSocialiserGenes.html
inst/xSocialiserNetplot.html
inst/xSocialiserSNPs.html
inst/xSparseMatrix.html
inst/xSubneterGR.html
inst/xSubneterGenes.html
inst/xSubneterSNPs.html
inst/xSymbol2GeneID.html
inst/xVisInterp.html
inst/xVisInterpAnimate.html
inst/xVisKernels.html
inst/xVisNet.html
man
man/ImmunoBase.Rd
man/JKscience_TS2A.Rd
man/eTerm.Rd
man/xCheckParallel.Rd
man/xCircos.Rd
man/xColormap.Rd
man/xConverter.Rd
man/xDAGanno.Rd
man/xDAGpropagate.Rd
man/xDAGsim.Rd
man/xDefineNet.Rd
man/xEnrichBarplot.Rd
man/xEnrichCompare.Rd
man/xEnrichConciser.Rd
man/xEnrichDAGplot.Rd
man/xEnrichDAGplotAdv.Rd
man/xEnrichNetplot.Rd
man/xEnrichViewer.Rd
man/xEnricher.Rd
man/xEnricherGenes.Rd
man/xEnricherSNPs.Rd
man/xEnricherYours.Rd
man/xFunArgs.Rd
man/xGR.Rd
man/xGR2GeneScores.Rd
man/xGR2nGenes.Rd
man/xGRsampling.Rd
man/xGRscores.Rd
man/xGRviaGeneAnno.Rd
man/xGRviaGenomicAnno.Rd
man/xGRviaGenomicAnnoAdv.Rd
man/xLiftOver.Rd
man/xRDataLoader.Rd
man/xRd2HTML.Rd
man/xRdWrap.Rd
man/xSM2DF.Rd
man/xSNP2GeneScores.Rd
man/xSNP2nGenes.Rd
man/xSNPlocations.Rd
man/xSNPscores.Rd
man/xSocialiser.Rd
man/xSocialiserDAGplot.Rd
man/xSocialiserDAGplotAdv.Rd
man/xSocialiserGenes.Rd
man/xSocialiserNetplot.Rd
man/xSocialiserSNPs.Rd
man/xSparseMatrix.Rd
man/xSubneterGR.Rd
man/xSubneterGenes.Rd
man/xSubneterSNPs.Rd
man/xSymbol2GeneID.Rd
man/xVisInterp.Rd
man/xVisInterpAnimate.Rd
man/xVisKernels.Rd
man/xVisNet.Rd
XGR documentation built on May 21, 2017, 12:23 a.m.