annGO                   Annotate the set of genes with the GO terms for
                        a given species and assembly
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 TCGA breast cancer RNAseq data.
calculateCorr           Calculates the correlation coefficient values
                        between two custom expression data.
convertGeneID           Convert gene ids according to the gene type
convertGMT              Convert gmt formatted pathway file to the
                        Pathway ID, Entrez, symbol formatted data frame
corrbased               Pearson correlation coefficient value of the
                        miRNA genes between miRNA:mRNA for a given
                        correlation cut-off and cancer.
corrbasedMrna           Pearson correlation coefficient value of the
                        mRNA genes between miRNA:mRNA for a given
                        correlation cut-off and cancer.
createNetwork           Create interaction network for top n enriched
                        GO term:coding RNA or GO-term:noncoding RNA
                        interaction. Nodes are GO term and RNA, edges
                        are interactions between them. Each GO-term is
                        annotated and enriched with the mRNAs provided
                        from the input list.
drawDotPlot             Draw dot plot of the enrichment object
extractBiotype          Get the biotype of the non-coding genes. It is
                        suitable for the GENCODE gtf files
filterBiotype           Extract the genes that have user provided
                        biotypes. This method is useful when input gene
                        list is mixed or when research of the interest
                        is only focused on specific group of genes.
geneGOEnricher          Given genes that fall in a given upstream and
                        downstream region of mRNAs of interest, GO term
                        enrichment analysis is carried out
genePathwayEnricher     Given genes that fall in the given upstream and
                        downstream region of mRNAs of interest, pathway
                        enrichment analysis is carried out
geneRegionGOEnricher    Given gene regions that fall in the given
                        upstream and downstream region of mRNAs of
                        interest, GO term enrichment analysis is
                        carried out
geneRegionPathwayEnricher
                        Given gene regions that fall in the given
                        upstream and downstream region of mRNAs of
                        interest, pathway enrichment analysis is
                        carried out
getGoDag                Plot and save the GO term DAG of the top n
                        enrichments in terms of p-values or adjusted
                        p-values with an user provided format
getKeggDiagram          Display the enriched KEGG diagram of the KEGG
                        pathway. This function is specific to only one
                        KEGG pathway id and identifies the enriched
                        genes in the diagram.
getmiRNACount           Get TCGA miRNAseq expression of miRNA genes for
                        the given cancer
getNearToExon           Get only those neighbouring genes that fall
                        within exon region
getNearToIntron         Get only those neighbouring genes that fall
                        within intron region
getReactomeDiagram      Display the enriched Reactome diagram of the
                        given Reactome pathway id. This function is
                        specific to only one pathway id and identifies
                        the enriched genes in the diagram.
getTADOverlap           For given region of interest, overlapped genes
                        in the TAD regions are found. Results can be
                        filtered according to the available cell lines.
getUCSC                 Get nearest genes for the window of the
                        upstream/downstream region.
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 fall in the given
                        upstream/downstream regions of the microRNA
                        genes
mirnaPathwayEnricher    Pathway enrichments of the microRNA genes with
                        mRNAs that fall in the given
                        upstream/downstream regions of the microRNA
                        genes
mirnaRegionGOEnricher   GO enrichments of the microRNA regions with
                        mRNAs that fall in the given
                        upstream/downstream regions of the microRNA
                        genes
mirnaRegionPathwayEnricher
                        Pathway enrichments of the microRNA regions
                        with mRNAs that fall in the given
                        upstream/downstream regions of the microRNA
                        genes
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 enrichment can be performed.
                        Function supports Entrez ID and symbol based
                        gmt file.
predictmiTargets        Predict the miRNA targets for the miRNA or mRNA
                        genes, which is specified with type parameter
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 for the given object and the order
                        type - p-value or adjusted p-value.
WikiEnrichment          WikiPathways Enrichment
writeEnrichment         Write the tabular form of the pathway or GO
                        term enrichment results
