ChIPpeakAnno-package | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
addAncestors | Add GO ids of the ancestors for a given vector of GO ids |
annotatedPeak | Annotated Peaks |
annotatePeakInBatch | obtain the distance to the nearest TSS, miRNA, exon et al for a list of peak intervals |
BED2RangedData | convert BED format to RangedData |
ChIPpeakAnno | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
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. |
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 |
GFF2RangedData | convert GFF format to RangedData |
makeVennDiagram | Make Venn Diagram from two peak ranges |
myPeakList | ChIP-seq peak dataset |
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.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 |
write2FASTA | write sequences to a file in fasta format |