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.


News

NEW FEATURES

o Change functions ('xEnrichBarplot' and 'xEnrichCompare') caused by the major ggplot2 update (2.2.0)

o Add function 'xColormap' for defining color palette (including those used by ggplot2)

o Add new functions ('xSubneterGR', 'xGR2GeneScores', 'xGR2nGenes' and 'xGRscores') to conduct region-based network analysis

o Populate annotations

NEW FEATURES

o Add infrastructure functions ('xSNPlocations' and 'xSM2DF')

o Populate annotations

NEW FEATURES

o Fix bugs in the function 'xRDataLoader' for Windows users

o Enable the choosing analysis resolution done by 'xGRviaGenomicAnno'

NEW FEATURES

o Add new functions ('xEnrichConciser', 'xEnrichBarplot', 'xEnrichDAGplot', 'xEnrichCompare' and 'xEnrichDAGplotAdv') to visualise and compare enrichment analysis results

o Add new functions ('xSocialiserDAGplot' and 'xSocialiserDAGplotAdv') to visualise and compare similarity analysis results

o Add new functions ('xVisKernels', 'xSNPscores', 'xSNP2nGenes', 'xSparseMatrix' and 'xSNP2GeneScores') to control how to define and score seed genes from a list of GWAS SNPs

o Add annotation functions ('xGRviaGeneAnno', 'xGRviaGenomicAnno' and 'xGRviaGenomicAnnoAdv') to interpret user-defined list of genomic regions either via looking at nearby gene annotations by ontologies or via looking at co-localised functional genomic annotations

NEW FEATURES

o A new data interpretation system by comprehensively utilising ontology and network information to make a user-defined gene or SNP list more interpretable

o Enrichment analysis using either built-in or custom ontologies

o Similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles

o Network analysis for identifying gene networks given a query list of (significant) genes or SNPs

Reference manual

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install.packages("XGR")

1.0.10 by Hai Fang, 7 months ago


http://XGR.r-forge.r-project.org, http://galahad.well.ox.ac.uk/XGR, http://rpubs.com/hfang/XGR


Report a bug at https://github.com/hfang-bristol/XGR/issues


Browse source code at https://github.com/cran/XGR


Authors: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight


Documentation:   PDF Manual  


GPL-2 license


Imports Matrix, RCircos, grDevices, graphics, GenomicRanges, IRanges, S4Vectors, supraHex, rtracklayer, stats, BiocGenerics, plot3D

Depends on igraph, dnet, ggplot2

Suggests foreach, doParallel, akima


See at CRAN