BED2RangedData          convert BED format to RangedData
ChIPpeakAnno-package    Batch annotation of the peaks identified from
                        either ChIP-seq or ChIP-chip experiments.
ExonPlusUtr.human.GRCh37
                        Gene model with exon, 5' UTR and 3' UTR
                        information for human sapiens (GRCh37) obtained
                        from biomaRt
GFF2RangedData          convert GFF format to RangedData
Peaks.Ste12.Replicate1
                        Ste12-binding sites from biological replicate 1
                        in yeast (see reference)
Peaks.Ste12.Replicate2
                        Ste12-binding sites from biological replicate 2
                        in yeast (see reference)
Peaks.Ste12.Replicate3
                        Ste12-binding sites from biological replicate 3
                        in yeast (see reference)
TSS.human.GRCh37        TSS annotation for human sapiens (GRCh37)
                        obtained from biomaRt
TSS.human.NCBI36        TSS annotation for human sapiens (NCBI36)
                        obtained from biomaRt
TSS.mouse.NCBIM37       TSS annotation data for mouse (NCBIM37)
                        obtained from biomaRt
TSS.rat.RGSC3.4         TSS annotation data for rat (RGSC3.4) obtained
                        from biomaRt
TSS.zebrafish.Zv8       TSS annotation data for zebrafish (Zv8)
                        obtained from biomaRt
addAncestors            Add GO ids of the ancestors for a given vector
                        of GO ids
annotatePeakInBatch     obtain the distance to the nearest TSS, miRNA,
                        exon et al for a list of peak intervals
annotatedPeak           Annotated Peaks
convert2EntrezID        Convert other common IDs such as ensemble gene
                        id, gene symbol, refseq id to entrez gene ID.
enrichedGO              Enriched Gene Ontology terms used as example
findOverlappingPeaks    Find the overlapping peaks for two peak ranges.
findVennCounts          Obtain Counts for Venn Diagram, internal
                        function for makeVennDigram
getAllPeakSequence      Obtain genomic sequences around the peaks
getAnnotation           Obtain the TSS, exon or miRNA annotation for
                        the specified species
getEnrichedGO           Obtain enriched gene ontology (GO) terms that
                        near the peaks
makeVennDiagram         Make Venn Diagram from two peak ranges
myPeakList              ChIP-seq peak dataset
write2FASTA             write sequences to a file in fasta format
