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| eTerm | Definition for S3 class 'eTerm' |
| ImmunoBase | Immune-disease associated variants, regions and genes from ImmunoBase (hg19) |
| JKscience_TS2A | Table S2A for cis-eQTLs among shared datasets from Benjamin et al. (2014) |
| print.eTerm | Definition for S3 class 'eTerm' |
| xCheckParallel | Function to check whether parallel computing should be used and how |
| xCircos | Function to visualise a network as a circos plot |
| xColormap | Function to define a colormap |
| xConverter | Function to convert an object between graph classes |
| xDAGanno | Function to generate a subgraph of a direct acyclic graph (DAG) induced by the input annotation data |
| xDAGpropagate | Function to generate a subgraph of a direct acyclic graph (DAG) propagaged by the input annotation data |
| xDAGsim | Function to calculate pair-wise semantic similarity between input terms based on a direct acyclic graph (DAG) with annotated data |
| xDefineNet | Function to define a gene network |
| xEnrichBarplot | Function to visualise enrichment results using a barplot |
| xEnrichCompare | Function to compare enrichment results using side-by-side barplots |
| xEnrichConciser | Function to make enrichment results conciser by removing redundant terms |
| xEnrichDAGplot | Function to visualise enrichment results using a direct acyclic graph (DAG) |
| xEnrichDAGplotAdv | Function to visualise comparative enrichment results using a direct acyclic graph (DAG) |
| xEnricher | Function to conduct enrichment analysis given the input data and the ontology and its annotation |
| xEnricherGenes | Function to conduct enrichment analysis given a list of genes and the ontology in query |
| xEnricherSNPs | Function to conduct enrichment analysis given a list of SNPs and the ontology in query |
| xEnricherYours | Function to conduct enrichment analysis given YOUR own input data |
| xEnrichNetplot | Function to visualise enrichment results using different network layouts |
| xEnrichViewer | Function to view enrichment results |
| xFunArgs | Function to assign (and evaluate) arguments with default values for a given function |
| xGR | Function to create a GRanges object given a list of genomic regions |
| xGR2GeneScores | Function to identify likely modulated seed genes given a list of genomic regions together with the significance level |
| xGR2nGenes | Function to define nearby genes given a list of genomic regions |
| xGRsampling | Function to generate random samples for data genomic regions from background genomic regions |
| xGRscores | Function to score genomic regions based on the given significance level |
| xGRviaGeneAnno | Function to conduct region-based enrichment analysis using nearby gene annotations |
| xGRviaGenomicAnno | Function to conduct region-based enrichment analysis using genomic annotations via binomial test |
| xGRviaGenomicAnnoAdv | Function to conduct region-based enrichment analysis using genomic annotations via sampling |
| xLiftOver | Function to lift genomic intervals from one genome build to another. |
| xRd2HTML | Function to convert Rd files to HTML files |
| xRDataLoader | Function to load the package built-in RData |
| xRdWrap | Function to wrap texts from Rd files |
| xSM2DF | 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) |
| 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 significance level |
| xSocialiser | Function to calculate pair-wise semantic similarity given the input data and the ontology and its annotation |
| xSocialiserDAGplot | Function to draw DAG plot for visualising terms used to annotate an input SNP or gene |
| xSocialiserDAGplotAdv | Function to draw DAG plot for comparing two sets of terms used to annotate two SNPs or genes in query |
| xSocialiserGenes | Function to calculate pair-wise semantic similarity given a list of genes and the ontology in query |
| 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 |
| xSparseMatrix | Function to create a sparse matrix for an input file with three columns |
| xSubneterGenes | Function to identify a subnetwork from an input network and the signficance level imposed on its nodes |
| xSubneterGR | Function to identify a gene network from an input network given a list of genomic regions together with the significance level |
| xSubneterSNPs | 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) |
| xSymbol2GeneID | Function to convert gene symbols to entrez geneid |
| xVisInterp | Function to visualise interpolated irregular data |
| xVisKernels | Function to visualise distance kernel functions |
| xVisNet | Function to visualise a graph object of class "igraph" |