Man pages for hfang-bristol/XGR
Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

aOntoDefinition for S3 class 'aOnto'
bLDDefinition for S3 class 'bLD'
cModuleDefinition for S3 class 'cModule'
cPathDefinition for S3 class 'cPath'
DRDefinition for S3 class 'DR'
eTermDefinition for S3 class 'eTerm'
Haploid_regulatorsHaploid mutagenesis screens for regulators of protein...
ImmunoBaseImmune-disease associated variants, regions and genes from...
JKscience_TS2ATable S2A for cis-eQTLs among shared datasets from Benjamin...
ls_eTermDefinition for S3 class 'ls_eTerm'
mSeedDefinition for S3 class 'mSeed'
xAddCoordsFunction to add coordinates into a graph according to a node...
xAggregateFunction to aggregate data respecting number of features
xBicreateFunction to create a bipartitle graph
xBigraphFunction to obtain communities from a bipartitle graph
xBiheatmapFunction to visualise bipartitle graph communities using...
xBiprojectFunction to obtain a projected graph from a bipartitle graph
xCheckParallelFunction to check whether parallel computing should be used...
xCircosFunction to visualise a network as a circos plot
xColormapFunction to define a colormap
xCombineNetFunction to combine networks from a list of igraph objects
xConverterFunction to convert an object between graph classes
xCorrelationFunction to calculate and visualise correlation
xCrosstalkFunction to identify a pathway crosstalk
xDAGannoFunction to generate a subgraph of a direct acyclic graph...
xDAGpropagateFunction to generate a subgraph of a direct acyclic graph...
xDAGsimFunction to calculate pair-wise semantic similarity between...
xDefineEQTLFunction to extract eQTL-gene pairs given a list of SNPs or a...
xDefineGenomicAnnoFunction to define genomic annotations
xDefineHICFunction to extract promoter capture HiC-gene pairs given a...
xDefineNetFunction to define a gene network
xDefineOntologyFunction to define ontology and its annotations
xEnrichBarplotFunction to visualise enrichment results using a barplot
xEnrichCompareFunction to compare enrichment results using side-by-side...
xEnrichConciserFunction to make enrichment results conciser by removing...
xEnrichDAGplotFunction to visualise enrichment results using a direct...
xEnrichDAGplotAdvFunction to visualise comparative enrichment results using a...
xEnricherFunction to conduct enrichment analysis given the input data...
xEnricherGenesFunction to conduct enrichment analysis given a list of genes...
xEnricherGenesAdvFunction to conduct enrichment analysis given a list of gene...
xEnricherSNPsFunction to conduct enrichment analysis given a list of SNPs...
xEnricherYoursFunction to conduct enrichment analysis given YOUR own input...
xEnrichForestFunction to visualise enrichment results using a forest plot
xEnrichHeatmapFunction to visualise enrichment results using heatmap
xEnrichLadderFunction to visualise enrichment results using ladder-like...
xEnrichMatrixFunction to compare enrichment results using matrix plots
xEnrichNetplotFunction to visualise enrichment results using different...
xEnrichRadialFunction to visualise enrichment results using radial-like...
xEnrichTreemapFunction to visualise enrichment results using a treemap
xEnrichViewerFunction to view enrichment results
xFunArgsFunction to assign (and evaluate) arguments with default...
xGGnetworkFunction to visualise an igraph object using ggnetwork
xGRFunction to create a GRanges object given a list of genomic...
xGR2GeneScoresFunction to identify likely modulated seed genes given a list...
xGR2nGenesFunction to define nearby genes given a list of genomic...
xGR2xGeneAnnoFunction to conduct region-based enrichment analysis via...
xGR2xGeneAnnoAdvFunction to conduct region-based enrichment analysis via...
xGR2xGenesFunction to define genes from an input list of genomic...
xGR2xGeneScoresFunction to identify likely modulated seed genes from an...
xGR2xNetFunction to identify a gene network from an input network...
xGraphMLFunction to generate a graphml file from a graph object of...
xGraphSplitFunction to split a graph according to a node attribute
xGRcseFunction to create a vector storing genomic regions
xGRkaryogramFunction to visualise genomic regions using karyogram plot
xGRmanhattanFunction to visualise genomic regions using manhattan plot
xGRoverlapFunction to extract overlap-based scores given genomic...
xGRsamplingFunction to generate random samples for data genomic regions...
xGRscoresFunction to score genomic regions based on the given...
xGRsepFunction to obtain separator index.
xGRsortFunction to sort by chromosomes/seqnames, start and end...
xGRtrackFunction to visualise genes within a genomic region using...
xGRviaGeneAnnoFunction to conduct region-based enrichment analysis using...
xGRviaGeneAnnoAdvFunction to conduct region-based enrichment analysis given a...
xGRviaGenomicAnnoFunction to conduct region-based enrichment analysis using...
xGRviaGenomicAnnoAdvFunction to conduct region-based enrichment analysis using...
xGScoreFunction to extract scores given a list of genomic regions
xGScoreAdvFunction to calculate per base scores given a list of genomic...
xGTFunction to plot a tree and its clades
xGTheatmapFunction to plot heatmap given associated data on tree tips
xGTheatmapAdvFunction to plot tree and heatmap given associated data on...
xGTplotFunction to plot tree with associated data on tips
xHeatmapFunction to draw heatmap using ggplot2
xHeatmapAdvFunction to draw heatmap together with sidebars on rows using...
xHEBFunction to visualise a graph with communities using...
xLayoutFunction to define graph node coordinates according to...
xLDblockFunction to obtain LD blocks
xLDenricherFunction to conduct LD-based enrichment analysis using...
xLDsamplingFunction to generate randomly sampled LD blocks
xLiftOverFunction to lift genomic intervals from one genome build to...
xObjSizeFunction to estimate memory allocated for an R variable or a...
xOBOcodeFunction to create codes annotating nodes in an igraph object
xPCHiCplotFunction to visualise promoter capture HiC data using...
xPolarBarFunction to visualise a data frame using a polar barplot
xPolarDotFunction to visualise a data frame using a polar dotplot
xRd2HTMLFunction to convert Rd files to HTML files
xRDataLoaderFunction to load the package built-in RData
xRdWrapFunction to wrap texts from Rd files
xRegressFunction to regress data according to principle components...
xRepurposeFunction to obtain repurposing matrix
xRPSFunction to calculate regulatory potential scores for genomic...
xRWenricherFunction to perform connectivity enrichment analysis on the...
xRWkernelFunction to calculate random walk kernel on the input graph
xSimplifyNetFunction to simplify networks from an igraph object
xSM2DFFunction to create a data frame (with three columns) from a...
xSNP2cGenesFunction to define HiC genes given a list of SNPs
xSNP2eGenesFunction to define eQTL genes given a list of SNPs or a...
xSNP2GeneScoresFunction to identify likely modulated seed genes given a list...
xSNP2nGenesFunction to define nearby genes given a list of SNPs
xSNPlocationsFunction to extract genomic locations given a list of SNPs
xSNPscoresFunction to score lead or LD SNPs based on the given...
xSocialiserFunction to calculate pair-wise semantic similarity given the...
xSocialiserDAGplotFunction to draw DAG plot for visualising terms used to...
xSocialiserDAGplotAdvFunction to draw DAG plot for comparing two sets of terms...
xSocialiserGenesFunction to calculate pair-wise semantic similarity given a...
xSocialiserNetplotFunction to visualise terms used to annotate an input SNP or...
xSocialiserSNPsFunction to calculate pair-wise semantic similarity given a...
xSparseMatrixFunction to create a sparse matrix for an input file with...
xSubneterGenesFunction to identify a subnetwork from an input network and...
xSubneterGRFunction to identify a gene network from an input network...
xSubneterSNPsFunction to identify a gene network from an input network...
xSymbol2GeneIDFunction to convert gene symbols to entrez geneid
xVisInterpFunction to visualise interpolated irregular data
xVisInterpAnimateFunction to animate the visualisation of interpolated...
xVisKernelsFunction to visualise distance kernel functions
xVisNetFunction to visualise a graph object of class "igraph"
xVolcanoFunction to draw a volcano plot
xWCNFunction to perform weighted gene correlated network analysis
xWCNheatmapFunction to draw heatmap from a cModule object
hfang-bristol/XGR documentation built on Nov. 18, 2018, 2:37 a.m.