getGeneSeq: Get gene sequence using the biomaRt package.getEnrichedPATH: Obtain enriched PATH that near the peaks.getEnrichedGO: Obtain enriched gene ontology (GO) terms that near the peaks.getAnnotation: Obtain the TSS, exon or miRNA annotation for the specified.getAllPeakSequence: Obtain genomic sequences around the peaks.genomicElementUpSetR: Genomic Element data for upset plot.genomicElementDistribution: Genomic Element distribution.findOverlapsOfPeaks: Find the overlapped peaks among two or more set of peaks.findOverlappingPeaks: Find the overlapping peaks for two peak ranges.findMotifsInPromoterSeqs: Find occurence of input motifs in the promoter regions of the.findEnhancers: Find possible enhancers depend on DNA interaction data.featureAlignedSignal: extract signals in given ranges.featureAlignedHeatmap: Heatmap representing signals in given ranges.featureAlignedExtendSignal: extract signals in given ranges from bam files.featureAlignedDistribution: plot distribution in given ranges.37: Gene model with exon, 5' UTR and 3' UTR information for human.estFragmentLength: estimate the fragment length.enrichmentPlot: plot enrichment results.enrichedGO: Enriched Gene Ontology terms used as example.egOrgMap: Convert between the name of the organism annotation package.downstreams: Get downstream coordinates.

cumulativePercentage: Plot the cumulative percentage tag allocation in sample.countPatternInSeqs: Output total number of patterns found in the input sequences.convert2EntrezID: Convert other common IDs to entrez gene ID.condenseMatrixB圜olnames: Condense matrix by colnames.

ChIPpeakAnno-package: Batch annotation of the peaks identified from either ChIP-seq.ChIPpeakAnno-deprecated: Deprecated Functions in Package ChIPpeakAnno.

binOverRegions: coverage of chromosome regions.

binOverFeature: Aggregate peaks over bins from the TSS.

bdp: obtain the peaks near bi-directional promoters.

assignChromosomeRegion: Summarize peak distribution over exon, intron, enhancer.

annotatePeakInBatch: Obtain the distance to the nearest TSS, miRNA, and/or exon.

addMetadata: Add metadata of the GRanges objects used for.

addGeneIDs: Add common IDs to annotated peaks such as gene symbol, entrez.

addAncestors: Add GO IDs of the ancestors for a given vector of GO ids.

Mestrenova peak annotation