BED2RangedData Convert BED format to RangedData ChIPpeakAnno-deprecated Deprecated Functions in Package ChIPpeakAnno 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 HOT.spots High Occupancy of Transcription Related Factors regions 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.GRCh38 TSS annotation for human sapiens (GRCh38) obtained from biomaRt TSS.human.NCBI36 TSS annotation for human sapiens (NCBI36) obtained from biomaRt TSS.mouse.GRCm38 TSS annotation data for Mus musculus (GRCm38.p1) 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.rat.Rnor_5.0 TSS annotation data for Rattus norvegicus (Rnor_5.0) obtained from biomaRt TSS.zebrafish.Zv8 TSS annotation data for zebrafish (Zv8) obtained from biomaRt TSS.zebrafish.Zv9 TSS annotation for Danio rerio (Zv9) obtained from biomaRt addAncestors Add GO IDs of the ancestors for a given vector of GO ids addGeneIDs Add common IDs to annotated peaks such as gene symbol, entrez ID, ensemble gene id and refseq id. annoGR-class Class 'annoGR' annotatePeakInBatch Obtain the distance to the nearest TSS, miRNA, and/or exon for a list of peaks annotatedPeak Annotated Peaks assignChromosomeRegion Summarize peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR binOverFeature Aggregate peaks over bins from the TSS bindist-class Class '"bindist"' condenseMatrixByColnames Condense matrix by colnames convert2EntrezID Convert other common IDs to entrez gene ID. countPatternInSeqs Output total number of patterns found in the input sequences egOrgMap Convert between the name of the organism annotation package ("OrgDb") and the name of the organism. enrichedGO Enriched Gene Ontology terms used as example featureAlignedDistribution plot distribution in given ranges featureAlignedHeatmap Heatmap representing signals in given ranges featureAlignedSignal extract signals in given ranges findOverlappingPeaks Find the overlapping peaks for two peak ranges. findOverlapsOfPeaks Find the overlapped peaks among two or more set of peaks. findVennCounts Obtain Venn 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 getEnrichedPATH Obtain enriched PATH that near the peaks getVennCounts Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram makeVennDiagram Make Venn Diagram from a list of peaks mergePlusMinusPeaks Merge peaks from plus strand and minus strand myPeakList An example GRanges object representing a ChIP-seq peak dataset peakPermTest Permutation Test for two given peak lists peaksNearBDP obtain the peaks near bi-directional promoters permPool-class Class '"permPool"' pie1 Pie Charts preparePool prepare data for permutation test summarizePatternInPeaks Output a summary of the occurrence of each pattern in the sequences. toGRanges Convert dataset to GRanges translatePattern translate pattern from IUPAC Extended Genetic Alphabet to regular expression wgEncodeTfbsV3 transcription factor binding site clusters (V3) from ENCODE write2FASTA Write sequences to a file in fasta format