| 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 |
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