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

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The central goal of XGR is to provide a data interpretation system. 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.

Author
Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Date of publication
2016-11-24 00:29:40
Maintainer
Hai Fang <hfang@well.ox.ac.uk>
License
GPL-2
Version
1.0.5
URLs

View on CRAN

Man pages

ImmunoBase
Immune-disease associated variants, regions and genes from...
JKscience_TS2A
Table S2A for cis-eQTLs among shared datasets from Benjamin...
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...
xDAGsim
Function to calculate pair-wise semantic similarity between...
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...
xVisKernels
Function to visualise distance kernel functions
xVisNet
Function to visualise a graph object of class "igraph"

Files in this package

XGR
XGR/inst
XGR/inst/xLiftOver.html
XGR/inst/xEnricherYours.html
XGR/inst/xGRscores.html
XGR/inst/xSNP2GeneScores.html
XGR/inst/xEnricherGenes.html
XGR/inst/xGRviaGenomicAnno.html
XGR/inst/xSocialiserDAGplotAdv.html
XGR/inst/CITATION
XGR/inst/XGR.icon.png
XGR/inst/xSocialiserGenes.html
XGR/inst/xEnrichDAGplot.html
XGR/inst/xSNPlocations.html
XGR/inst/xRd2HTML.html
XGR/inst/ImmunoBase.html
XGR/inst/xSubneterSNPs.html
XGR/inst/xSubneterGR.html
XGR/inst/xConverter.html
XGR/inst/xGRviaGenomicAnnoAdv.html
XGR/inst/xGR2GeneScores.html
XGR/inst/xRdWrap.html
XGR/inst/xGRsampling.html
XGR/inst/NEWS
XGR/inst/xCircos.html
XGR/inst/xEnrichConciser.html
XGR/inst/xSNP2nGenes.html
XGR/inst/xColormap.html
XGR/inst/xSM2DF.html
XGR/inst/xGR2nGenes.html
XGR/inst/xEnricherSNPs.html
XGR/inst/xGRviaGeneAnno.html
XGR/inst/XGR.logo.png
XGR/inst/xSocialiserNetplot.html
XGR/inst/xEnrichNetplot.html
XGR/inst/xVisKernels.html
XGR/inst/xEnrichViewer.html
XGR/inst/xSparseMatrix.html
XGR/inst/xEnricher.html
XGR/inst/xDAGsim.html
XGR/inst/xEnrichCompare.html
XGR/inst/xEnrichDAGplotAdv.html
XGR/inst/xFunArgs.html
XGR/inst/xEnrichBarplot.html
XGR/inst/xRDataLoader.html
XGR/inst/JKscience_TS2A.html
XGR/inst/xDAGanno.html
XGR/inst/xGR.html
XGR/inst/xVisNet.html
XGR/inst/xSocialiserSNPs.html
XGR/inst/xSocialiserDAGplot.html
XGR/inst/xSNPscores.html
XGR/inst/xSubneterGenes.html
XGR/inst/xSocialiser.html
XGR/NAMESPACE
XGR/data
XGR/data/ImmunoBase.RData
XGR/data/JKscience_TS2A.RData
XGR/R
XGR/R/xLiftOver.r
XGR/R/xEnricherYours.r
XGR/R/xCircos.r
XGR/R/xSocialiser.r
XGR/R/xDAGsim.r
XGR/R/xEnrichDAGplotAdv.r
XGR/R/xConverter.r
XGR/R/xEnricherGenes.r
XGR/R/xGRviaGenomicAnno.r
XGR/R/xSNP2nGenes.r
XGR/R/xSNPscores.r
XGR/R/xSNPlocations.r
XGR/R/xEnricher.r
XGR/R/xEnrichCompare.r
XGR/R/xColormap.r
XGR/R/xSM2DF.r
XGR/R/xGR2GeneScores.r
XGR/R/xGR.r
XGR/R/xSocialiserNetplot.r
XGR/R/xRd2HTML.r
XGR/R/xVisNet.r
XGR/R/xDAGanno.r
XGR/R/xEnrichViewer.r
XGR/R/xSocialiserSNPs.r
XGR/R/xRdWrap.r
XGR/R/xEnrichNetplot.r
XGR/R/xGRviaGenomicAnnoAdv.r
XGR/R/xEnrichConciser.r
XGR/R/xEnricherSNPs.r
XGR/R/xEnrichBarplot.r
XGR/R/xVisKernels.r
XGR/R/xSocialiserGenes.r
XGR/R/xGRsampling.r
XGR/R/xSubneterSNPs.r
XGR/R/xSocialiserDAGplotAdv.r
XGR/R/xGRviaGeneAnno.r
XGR/R/xFunArgs.r
XGR/R/xSubneterGR.r
XGR/R/xSocialiserDAGplot.r
XGR/R/xSNP2GeneScores.r
XGR/R/xGR2nGenes.r
XGR/R/xGRscores.r
XGR/R/xRDataLoader.r
XGR/R/xSubneterGenes.r
XGR/R/xSparseMatrix.r
XGR/R/xEnrichDAGplot.r
XGR/MD5
XGR/DESCRIPTION
XGR/man
XGR/man/xVisKernels.Rd
XGR/man/xSNP2GeneScores.Rd
XGR/man/xDAGanno.Rd
XGR/man/xSocialiserGenes.Rd
XGR/man/xEnrichConciser.Rd
XGR/man/JKscience_TS2A.Rd
XGR/man/xEnricherYours.Rd
XGR/man/xGRviaGenomicAnno.Rd
XGR/man/xSNPscores.Rd
XGR/man/xGR2nGenes.Rd
XGR/man/xSM2DF.Rd
XGR/man/xSocialiserDAGplot.Rd
XGR/man/ImmunoBase.Rd
XGR/man/xSocialiserDAGplotAdv.Rd
XGR/man/xSocialiserNetplot.Rd
XGR/man/xGR.Rd
XGR/man/xEnrichCompare.Rd
XGR/man/xCircos.Rd
XGR/man/xEnrichBarplot.Rd
XGR/man/xEnrichDAGplotAdv.Rd
XGR/man/xDAGsim.Rd
XGR/man/xConverter.Rd
XGR/man/xGRviaGeneAnno.Rd
XGR/man/xEnrichNetplot.Rd
XGR/man/xSubneterGR.Rd
XGR/man/xSocialiserSNPs.Rd
XGR/man/xSubneterSNPs.Rd
XGR/man/xSocialiser.Rd
XGR/man/xColormap.Rd
XGR/man/xRdWrap.Rd
XGR/man/xRd2HTML.Rd
XGR/man/xVisNet.Rd
XGR/man/xEnricherGenes.Rd
XGR/man/xEnricherSNPs.Rd
XGR/man/xRDataLoader.Rd
XGR/man/xSubneterGenes.Rd
XGR/man/xSNPlocations.Rd
XGR/man/xFunArgs.Rd
XGR/man/xGRsampling.Rd
XGR/man/xGRscores.Rd
XGR/man/xEnricher.Rd
XGR/man/xGR2GeneScores.Rd
XGR/man/xSNP2nGenes.Rd
XGR/man/xEnrichDAGplot.Rd
XGR/man/xLiftOver.Rd
XGR/man/xGRviaGenomicAnnoAdv.Rd
XGR/man/xEnrichViewer.Rd
XGR/man/xSparseMatrix.Rd