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

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.

AuthorHai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Date of publication2017-01-14 01:11:46
MaintainerHai Fang <hfang@well.ox.ac.uk>
LicenseGPL-2
Version1.0.8
http://XGR.r-forge.r-project.org, http://galahad.well.ox.ac.uk/XGR
http://rpubs.com/hfang/XGR

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...

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...

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"

Functions

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

Files

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/xCheckParallel.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/xCheckParallel.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/xCheckParallel.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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.