Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.


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Documentation for package ‘ChIPpeakAnno’ version 1.2.15

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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