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XGR (version 1.1.5)

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

Description

The central goal of XGR by Fang et al. (2016) 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.

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Version

Install

install.packages('XGR')

Monthly Downloads

189

Version

1.1.5

License

GPL-2

Homepage

http://XGR.r-forge.r-project.org

Maintainer

Last Published

March 29th, 2019

Functions in XGR (1.1.5)

Function to convert Rd files to HTML files

Function to check whether parallel computing should be used and how

Function to visualise enrichment results using a chord plot

Function to visualise enrichment results using ladder-like plot

Function to generate a graphml file from a graph object of class "igraph"

Function to compare enrichment results using matrix plots

Function to visualise a network as a circos plot

Function to visualise enrichment results using a barplot

Function to conduct enrichment analysis given the input data and the ontology and its annotation

Function to conduct enrichment analysis given a list of genes and the ontology in query

Function to wrap texts from Rd files

Function to calculate pair-wise semantic similarity between input terms based on a direct acyclic graph (DAG) with annotated data

Function to generate a graphml file from a pathway upon query

Function to draw heatmap together with sidebars on rows using ggplot2

Function to define nearby genes given a list of SNPs

Function to draw heatmap using ggplot2

xDefineGenomicAnno

Function to define genomic annotations

Function to generate a subgraph of a direct acyclic graph (DAG) induced by the input annotation data

Function to extract promoter capture HiC-gene pairs given a list of SNPs

Immune-disease associated variants, regions and genes from ImmunoBase (hg19)

Function to generate a subgraph of a direct acyclic graph (DAG) propagaged by the input annotation data

Function to define a gene network

Function to extract eQTL-gene pairs given a list of SNPs or a customised eQTL mapping data

Function to visualise enrichment results using a D3 plot

Function to visualise enrichment results using a tree-like circular plot

Function to define a colormap

Function to draw a tree-like circular plot

Function to combine networks from a list of igraph objects

Function to convert an object between graph classes

xDefineOntology

Function to define ontology and its annotations

Function to compare enrichment results using side-by-side barplots

Function to visualise enrichment results using a treemap

Function to visualise enrichment results using dot-like plot

Function to visualise enrichment results using a forest plot

Function to visualise enrichment results using a direct acyclic graph (DAG)

xEnrichConciser

Function to make enrichment results conciser by removing redundant terms

xEnricherGenesAdv

Function to conduct enrichment analysis given a list of gene sets and a list of ontologies

Function to visualise an igraph object using ggnetwork

Function to conduct enrichment analysis given YOUR own input data

xEnrichDAGplotAdv

Function to visualise comparative enrichment results using a direct acyclic graph (DAG)

Function to extract genomic locations given a list of SNPs

Function to visualise an igraph object using ggraph

Function to view enrichment results

Function to create a vector storing genomic regions

Function to generate random samples for data genomic regions from background genomic regions

Function to define genes from an input list of genomic regions given the crosslink info

xGR2xGeneScores

Function to identify likely modulated seed genes from an input list of genomic regions together with the significance level given the crosslink info

Function to visualise enrichment results using a ggraph-like lauout

Function to visualise enrichment results using heatmap

Function to visualise enrichment results using different network layouts

Function to visualise enrichment results using radial-like plot

Function to conduct enrichment analysis given a list of SNPs and the ontology in query

Function to conduct region-based enrichment analysis via crosslinked genes

Function to identify likely modulated seed genes given a list of genomic regions together with the significance level

xGR2xGeneAnnoAdv

Function to conduct region-based enrichment analysis via crosslinked genes given a list of genomic region sets and a list of ontologies

Function to conduct region-based enrichment analysis using nearby gene annotations

Function to sort by chromosomes/seqnames, start and end coordinates of the intervals.

Function to estimate memory allocated for an R variable or a file

Function to load the package built-in RData

Function to define nearby genes given a list of genomic regions

Function to visualise data frame using pie plots

Function to create a GRanges object given a list of genomic regions

Function to create a data frame (with three columns) from a (sparse) matrix

xSNP2GeneScores

Function to identify likely modulated seed genes given a list of SNPs together with the significance level (e.g. GWAS reported p-values)

Function to generate a html-formatted report

Function to score genomic regions based on the given significance level

Function to convert gene symbols to entrez geneid

Function to define HiC genes given a list of SNPs

Function to obtain separator index.

xGRviaGeneAnnoAdv

Function to conduct region-based enrichment analysis given a list of genomic region sets and a list of ontologies

Function to calculate pair-wise semantic similarity given the input data and the ontology and its annotation

Function to define eQTL genes given a list of SNPs or a customised eQTL mapping data

xGRviaGenomicAnnoAdv

Function to conduct region-based enrichment analysis using genomic annotations via sampling

xSocialiserDAGplotAdv

Function to draw DAG plot for comparing two sets of terms used to annotate two SNPs or genes in query

xGRviaGenomicAnno

Function to conduct region-based enrichment analysis using genomic annotations via binomial test

Function to visualise distance kernel functions

Function to define graph node coordinates according to igraph- or sna-style layout

Function to convert gene symbols to entrez geneid

xSocialiserGenes

Function to calculate pair-wise semantic similarity given a list of genes and the ontology in query

Function to lift genomic intervals from one genome build to another.

Function to visualise a graph object of class "igraph"

Function to conduct colocalisation analysis through Wakefield's Approximate Bayes Factor approach integrating GWAS and eQTL summary data

Function to create codes annotating nodes in an igraph object

xSocialiserDAGplot

Function to draw DAG plot for visualising terms used to annotate an input SNP or gene

Function to score lead or LD SNPs based on the given significance level

Function to identify a subnetwork from an input network and the signficance level imposed on its nodes

Function to simplify networks from an igraph object

Function to identify a gene network from an input network given a list of seed SNPs together with the significance level (e.g. GWAS reported p-values)

xSocialiserNetplot

Function to visualise terms used to annotate an input SNP or gene using different network layouts

xSocialiserSNPs

Function to calculate pair-wise semantic similarity given a list of SNPs and the ontology in query

Function to create a sparse matrix for an input file with three columns

Function to identify a gene network from an input network given a list of genomic regions together with the significance level

Function to add coordinates into a graph according to a node attribute

Function to aggregate data respecting number of features

Function to assign (and evaluate) arguments with default values for a given function

Function to encode a file as a base64 string for embedding

Definition for S3 class ls_eTerm

Haploid_regulators

Haploid mutagenesis screens for regulators of protein phenotypes

Definition for S3 class eTerm

Definition for S3 class aOnto

Table S2A for cis-eQTLs among shared datasets from Benjamin et al. (2014)