| annGO | Annotate the set of genes with the GO terms for a given... |
| assembly | Get the required information for the given assembly |
| brain_disorder_ncRNA | Differentially expressed non-coding gene |
| brain_mirna | Differentially expressed human brain data |
| breastmRNA | Protein coding genes that are differentially expressed in... |
| calculateCorr | Calculates the correlation coefficient values between two... |
| convertGeneID | Convert gene ids according to the gene type |
| convertGMT | Convert gmt formatted pathway file to the Pathway ID, Entrez,... |
| corrbased | Pearson correlation coefficient value of the miRNA genes... |
| corrbasedMrna | Pearson correlation coefficient value of the mRNA genes... |
| createNetwork | Create interaction network for top n enriched GO term:coding... |
| drawDotPlot | Draw dot plot of the enrichment object |
| extractBiotype | Get the biotype of the non-coding genes. It is suitable for... |
| filterBiotype | Extract the genes that have user provided biotypes. This... |
| geneGOEnricher | Given genes that fall in a given upstream and downstream... |
| genePathwayEnricher | Given genes that fall in the given upstream and downstream... |
| geneRegionGOEnricher | Given gene regions that fall in the given upstream and... |
| geneRegionPathwayEnricher | Given gene regions that fall in the given upstream and... |
| getGoDag | Plot and save the GO term DAG of the top n enrichments in... |
| getKeggDiagram | Display the enriched KEGG diagram of the KEGG pathway. This... |
| getmiRNACount | Get TCGA miRNAseq expression of miRNA genes for the given... |
| getNearToExon | Get only those neighbouring genes that fall within exon... |
| getNearToIntron | Get only those neighbouring genes that fall within intron... |
| getReactomeDiagram | Display the enriched Reactome diagram of the given Reactome... |
| getTADOverlap | For given region of interest, overlapped genes in the TAD... |
| getUCSC | Get nearest genes for the window of the upstream/downstream... |
| goEnrichment | Perform enrichment analysis of the given genes |
| KeggEnrichment | KEGG pathway enrichment |
| listTAD | List cell line of the given topological domain regions |
| mirna | Brain miRNA expression retrieved from the TCGA |
| mirnaGOEnricher | GO term enrichments of the microRNA genes with mRNAs that... |
| mirnaPathwayEnricher | Pathway enrichments of the microRNA genes with mRNAs that... |
| mirnaRegionGOEnricher | GO enrichments of the microRNA regions with mRNAs that fall... |
| mirnaRegionPathwayEnricher | Pathway enrichments of the microRNA regions with mRNAs that... |
| mrna | Brain mRNA expression retrieved from the TCGA |
| ncRegion | Differentially expressed non-coding gene regions |
| NoRCE-class | An S4 class to represent enrichment |
| packageCheck | Check the package availability for the given assembly |
| pathwayEnrichment | For a given gmt file of a specific pathway database, pathway... |
| predictmiTargets | Predict the miRNA targets for the miRNA or mRNA genes, which... |
| reactomeEnrichment | Reactome pathway enrichment |
| setParameters | Set the parameters |
| tad_dmel | TAD regions for the fly |
| tad_hg19 | TAD regions for human hg19 assembly |
| tad_hg38 | TAD regions for human hg38 assembly |
| tad_mm10 | TAD regions for mouse |
| topEnrichment | Number of top enrichment results of the pathway or GO terms... |
| WikiEnrichment | WikiPathways Enrichment |
| writeEnrichment | Write the tabular form of the pathway or GO term enrichment... |
