| aOnto | Definition for S3 class 'aOnto' |
| EG | Definition for S3 class 'EG' |
| eTerm | Definition for S3 class 'eTerm' |
| GS | Definition for S3 class 'GS' |
| Haploid_regulators | Haploid mutagenesis screens for regulators of protein... |
| ImmunoBase | Immune-disease associated variants, regions and genes from... |
| iSubg | Definition for S3 class 'iSubg' |
| JKscience_TS2A | Table S2A for cis-eQTLs among shared datasets from Benjamin... |
| ls_eTerm | Definition for S3 class 'ls_eTerm' |
| xAddCoords | Function to add coordinates into a graph according to a node... |
| xAggregate | Function to aggregate data respecting number of features |
| xAuxEmbed | Function to encode a file as a base64 string for embedding |
| xAuxFunArgs | Function to assign (and evaluate) arguments with default... |
| xAuxRd2HTML | Function to convert Rd files to HTML files |
| xAuxRdWrap | Function to wrap texts from Rd files |
| 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 |
| xCombineNet | Function to combine networks from a list of igraph objects |
| xConverter | Function to convert an object between graph classes |
| xCtree | Function to draw a tree-like circular plot |
| xDAGanno | Function to generate a subgraph of a direct acyclic graph... |
| xDAGpropagate | Function to generate a subgraph of a direct acyclic graph... |
| xDAGsim | Function to calculate pair-wise semantic similarity between... |
| xDefineEQTL | Function to extract eQTL-gene pairs given a list of SNPs or a... |
| xDefineGenomicAnno | Function to define genomic annotations |
| xDefineHIC | Function to extract promoter capture HiC-gene pairs given a... |
| xDefineNet | Function to define a gene network |
| xDefineOntology | Function to define ontology and its annotations |
| xEnrichBarplot | Function to visualise enrichment results using a barplot |
| xEnrichChord | Function to visualise enrichment results using a chord plot |
| xEnrichCompare | Function to compare enrichment results using side-by-side... |
| xEnrichConciser | Function to make enrichment results conciser by removing... |
| xEnrichCtree | Function to visualise enrichment results using a tree-like... |
| xEnrichD3 | Function to visualise enrichment results using a D3 plot |
| xEnrichDAGplot | Function to visualise enrichment results using a direct... |
| xEnrichDAGplotAdv | Function to visualise comparative enrichment results using a... |
| xEnrichDotplot | Function to visualise enrichment results using dot-like plot |
| xEnricher | Function to conduct enrichment analysis given the input data... |
| xEnricherGenes | Function to conduct enrichment analysis given a list of genes... |
| xEnricherGenesAdv | Function to conduct enrichment analysis given a list of gene... |
| xEnricherSNPs | Function to conduct enrichment analysis given a list of SNPs... |
| xEnricherYours | Function to conduct enrichment analysis given YOUR own input... |
| xEnrichForest | Function to visualise enrichment results using a forest plot |
| xEnrichGGraph | Function to visualise enrichment results using a ggraph-like... |
| xEnrichHeatmap | Function to visualise enrichment results using heatmap |
| xEnrichLadder | Function to visualise enrichment results using ladder-like... |
| xEnrichMatrix | Function to compare enrichment results using matrix plots |
| xEnrichNetplot | Function to visualise enrichment results using different... |
| xEnrichRadial | Function to visualise enrichment results using radial-like... |
| xEnrichTreemap | Function to visualise enrichment results using a treemap |
| xEnrichViewer | Function to view enrichment results |
| xGeneID2Symbol | Function to convert gene symbols to entrez geneid |
| xGGnetwork | Function to visualise an igraph object using ggnetwork |
| xGGraph | Function to visualise an igraph object using ggraph |
| 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... |
| xGR2xGeneAnno | Function to conduct region-based enrichment analysis via... |
| xGR2xGeneAnnoAdv | Function to conduct region-based enrichment analysis via... |
| xGR2xGenes | Function to define genes from an input list of genomic... |
| xGR2xGeneScores | Function to identify likely modulated seed genes from an... |
| xGraphML | Function to generate a graphml file from a graph object of... |
| xGraphML2AA | Function to generate a graphml file from a pathway upon query |
| xGRcse | Function to create a vector storing genomic regions |
| xGRsampling | Function to generate random samples for data genomic regions... |
| xGRscores | Function to score genomic regions based on the given... |
| xGRsep | Function to obtain separator index. |
| xGRsort | Function to sort by chromosomes/seqnames, start and end... |
| xGRviaGeneAnno | Function to conduct region-based enrichment analysis using... |
| xGRviaGeneAnnoAdv | Function to conduct region-based enrichment analysis given a... |
| xGRviaGenomicAnno | Function to conduct region-based enrichment analysis using... |
| xGRviaGenomicAnnoAdv | Function to conduct region-based enrichment analysis using... |
| xHeatmap | Function to draw heatmap using ggplot2 |
| xHeatmapAdv | Function to draw heatmap together with sidebars on rows using... |
| xLayout | Function to define graph node coordinates according to... |
| xLiftOver | Function to lift genomic intervals from one genome build to... |
| xMarkNet | Function to mark a network within another network |
| xMEabf | Function to conduct colocalisation analysis through... |
| xObjSize | Function to estimate memory allocated for an R variable or a... |
| xOBOcode | Function to create codes annotating nodes in an igraph object |
| xPieplot | Function to visualise data frame using pie plots |
| xRDataLoader | Function to load the package built-in RData |
| xReport | Function to generate a html-formatted report |
| xSimplifyNet | Function to simplify networks from an igraph object |
| xSM2DF | Function to create a data frame (with three columns) from a... |
| xSNP2cGenes | Function to define HiC genes given a list of SNPs |
| xSNP2eGenes | Function to define eQTL genes given a list of SNPs or 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... |
| xSubneterGenesAdv | Function to iteratively identify subnetworks from an input... |
| xSubneterGenesMST | Function to identify a minimum spanning tree for subnetworks |
| xSubneterGR | Function to identify a gene network from an input network... |
| xSubneterSNPs | Function to identify a gene network from an input network... |
| xSymbol2GeneID | Function to convert gene symbols to entrez geneid |
| xVisKernels | Function to visualise distance kernel functions |
| xVisNet | Function to visualise a graph object of class "igraph" |
