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| ChIPpeakAnno-package | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
| $-method | Class '"bindist"' |
| $-method | Class '"permPool"' |
| $<--method | Class '"bindist"' |
| $<--method | Class '"permPool"' |
| 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 'annoGR' |
| annoGR-class | Class 'annoGR' |
| annoGR-method | Class 'annoGR' |
| annotatedPeak | Annotated Peaks |
| annotatePeakInBatch | Obtain the distance to the nearest TSS, miRNA, and/or exon for a list of peaks |
| assignChromosomeRegion | Summarize peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR |
| BED2RangedData | Convert BED format to RangedData |
| BED2RangedData-deprecated | Convert BED format to RangedData |
| bindist | Class '"bindist"' |
| bindist-class | Class '"bindist"' |
| bindist-method | Class '"bindist"' |
| binOverFeature | Aggregate peaks over bins from the TSS |
| ChIPpeakAnno | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
| ChIPpeakAnno-deprecated | Deprecated Functions in Package ChIPpeakAnno |
| coerce-method | Class 'annoGR' |
| 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 |
| ExonPlusUtr.human.GRCh37 | Gene model with exon, 5' UTR and 3' UTR information for human sapiens (GRCh37) obtained from biomaRt |
| 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. |
| findOverlappingPeaks-deprecated | 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 |
| GFF2RangedData | Convert GFF format to RangedData |
| GFF2RangedData-deprecated | Convert GFF format to RangedData |
| HOT.spots | High Occupancy of Transcription Related Factors regions |
| info | Class 'annoGR' |
| info-method | Class 'annoGR' |
| 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 |
| 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) |
| peaksNearBDP | obtain the peaks near bi-directional promoters |
| permPool | Class '"permPool"' |
| permPool-class | Class '"permPool"' |
| permPool-method | 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 |
| 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 |
| wgEncodeTfbsV3 | transcription factor binding site clusters (V3) from ENCODE |
| write2FASTA | Write sequences to a file in fasta format |