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

aOntoDefinition for S3 class 'aOnto'
EGDefinition for S3 class 'EG'
eTermDefinition for S3 class 'eTerm'
GSDefinition for S3 class 'GS'
Haploid_regulatorsHaploid mutagenesis screens for regulators of protein...
ImmunoBaseImmune-disease associated variants, regions and genes from...
iSubgDefinition for S3 class 'iSubg'
JKscience_TS2ATable S2A for cis-eQTLs among shared datasets from Benjamin...
ls_eTermDefinition for S3 class 'ls_eTerm'
xAddCoordsFunction to add coordinates into a graph according to a node...
xAggregateFunction to aggregate data respecting number of features
xAuxEmbedFunction to encode a file as a base64 string for embedding
xAuxFunArgsFunction to assign (and evaluate) arguments with default...
xAuxRd2HTMLFunction to convert Rd files to HTML files
xAuxRdWrapFunction to wrap texts from Rd files
xAuxSIFunction to collect information on the R session
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
xCtreeFunction to draw a tree-like circular plot
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
xEnrichChordFunction to visualise enrichment results using a chord plot
xEnrichCompareFunction to compare enrichment results using side-by-side...
xEnrichConciserFunction to make enrichment results conciser by removing...
xEnrichCtreeFunction to visualise enrichment results using a tree-like...
xEnrichD3Function to visualise enrichment results using a D3 plot
xEnrichDAGplotFunction to visualise enrichment results using a direct...
xEnrichDAGplotAdvFunction to visualise comparative enrichment results using a...
xEnrichDotplotFunction to visualise enrichment results using dot-like plot
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
xEnrichGGraphFunction to visualise enrichment results using a ggraph-like...
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
xGeneID2SymbolFunction to convert gene symbols to entrez geneid
xGGnetworkFunction to visualise an igraph object using ggnetwork
xGGraphFunction to visualise an igraph object using ggraph
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...
xGraphMLFunction to generate a graphml file from a graph object of...
xGraphML2AAFunction to generate a graphml file from a pathway upon query
xGRcseFunction to create a vector storing genomic regions
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...
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...
xHeatmapFunction to draw heatmap using ggplot2
xHeatmapAdvFunction to draw heatmap together with sidebars on rows using...
xIG2TBFunction to convert an igraph into a tibble for nodes or...
xLayoutFunction to define graph node coordinates according to...
xLiftOverFunction to lift genomic intervals from one genome build to...
xMakeGenesFunction to prepare a gene_info RDS file
xMakeGenesetsFunction to prepare a gene_info RDS file
xMarkNetFunction to mark a network within another network
xMEabfFunction to conduct colocalisation analysis through...
xObjSizeFunction to estimate memory allocated for an R variable or a...
xOBOcodeFunction to create codes annotating nodes in an igraph object
xPieplotFunction to visualise data frame using pie plots
xRDataLoaderFunction to load the package built-in RData
xRDSFunction to read RDS files
xReportFunction to generate a html-formatted report
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...
xSubneterGenesAdvFunction to iteratively identify subnetworks from an input...
xSubneterGenesMSTFunction to identify a minimum spanning tree for subnetworks
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
xTB2IGFunction to convert an igraph from one or two tibbles
xVisKernelsFunction to visualise distance kernel functions
xVisNetFunction to visualise a graph object of class "igraph"
hfang-bristol/XGR documentation built on June 26, 2020, 1:26 a.m.