xAddCoords |
Function to add coordinates into a graph according to a node attribute |
xAggregate |
Function to aggregate data respecting number of features |
xBigraph |
Function to obtain communities from a bipartitle graph |
xBiheatmap |
Function to visualise bipartitle graph communities using heatmap |
xBiproject |
Function to obtain a projected graph from a bipartitle graph |
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 |
xCombineNet |
Function to combine networks from a list of igraph objects |
xConverter |
Function to convert an object between graph classes |
xCorrelation |
Function to calculate and visualise correlation |
xCrosstalk |
Function to identify a pathway crosstalk |
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 |
xDefineEQTL |
Function to extract eQTL-gene pairs given a list of SNPs or a customised eQTL mapping data |
xDefineGenomicAnno |
Function to define genomic annotations |
xDefineHIC |
Function to extract promoter capture HiC-gene pairs given a list of SNPs |
xDefineNet |
Function to define a gene network |
xDefineOntology |
Function to define ontology and its annotations |
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 |
xEnricherGenesAdv |
Function to conduct enrichment analysis given a list of gene sets and a list of ontologies |
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 |
xEnrichForest |
Function to visualise enrichment results using a forest plot |
xEnrichHeatmap |
Function to visualise enrichment results using heatmap |
xEnrichLadder |
Function to visualise enrichment results using ladder-like plot |
xEnrichMatrix |
Function to compare enrichment results using matrix plots |
xEnrichNetplot |
Function to visualise enrichment results using different network layouts |
xEnrichTreemap |
Function to visualise enrichment results using a treemap |
xEnrichViewer |
Function to view enrichment results |
xFunArgs |
Function to assign (and evaluate) arguments with default values for a given function |
xGGnetwork |
Function to visualise an igraph object using ggnetwork |
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 |
xGR2xGeneAnno |
Function to conduct region-based enrichment analysis via crosslinked genes |
xGR2xGeneAnnoAdv |
Function to conduct region-based enrichment analysis via crosslinked genes given a list of genomic region sets and a list of ontologies |
xGR2xGenes |
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 |
xGR2xNet |
Function to identify a gene network from an input network given a list of genomic regions |
xGraphML |
Function to generate a graphml file from a graph object of class "igraph" |
xGraphSplit |
Function to split a graph according to a node attribute |
xGRcse |
Function to create a vector for genomic regions |
xGRkaryogram |
Function to visualise genomic regions using karyogram plot |
xGRmanhattan |
Function to visualise genomic regions using manhattan plot |
xGRoverlap |
Function to extract overlap-based scores 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 |
xGRsep |
Function to obtain separator index. |
xGRsort |
Function to sort by chromosomes/seqnames, start and end coordinates of the intervals. |
xGRtrack |
Function to visualise genes within a genomic region using track plot |
xGRviaGeneAnno |
Function to conduct region-based enrichment analysis using nearby gene annotations |
xGRviaGeneAnnoAdv |
Function to conduct region-based enrichment analysis given a list of genomic region sets and a list of ontologies |
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 |
xGScore |
Function to extract scores given a list of genomic regions |
xGScoreAdv |
Function to calculate per base scores given a list of genomic regions in terms of overlaps with genomic annotations |
xHeatmap |
Function to draw heatmap using ggplot2 |
xHeatmapAdv |
Function to draw heatmap together with sidebars on rows using ggplot2 |
xHEB |
Function to visualise a graph with communities using hierarchical edge bundling |
xLDblock |
Function to obtain LD blocks |
xLDenricher |
Function to conduct LD-based enrichment analysis using genomic annotations via sampling |
xLDsampling |
Function to generate randomly sampled LD blocks |
xLiftOver |
Function to lift genomic intervals from one genome build to another. |
xOBOcode |
Function to create codes annotating nodes in an igraph object |
xPCHiCplot |
Function to visualise promoter capture HiC data using different network layouts |
xPolarBar |
Function to visualise a data frame using a polar barplot |
xPolarDot |
Function to visualise a data frame using a polar dotplot |
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 |
xRegress |
Function to regress data according to principle components (PCs) |
xRPS |
Function to calculate regulatory potential scores for genomic regions using genomic annotations |
xRWenricher |
Function to perform connectivity enrichment analysis on the input graph |
xRWkernel |
Function to calculate random walk kernel on the input graph |
xSimplifyNet |
Function to simplify networks from an igraph object |
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 |
xVisInterpAnimate |
Function to animate the visualisation of interpolated irregular data |
xVisKernels |
Function to visualise distance kernel functions |
xVisNet |
Function to visualise a graph object of class "igraph" |
xVolcano |
Function to draw a volcano plot |