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ChIPpeakAnno (version 2.16.4)

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges.

Description

The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs). This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages

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Version

Version

2.16.4

License

GPL (>= 2)

Maintainer

Lihua Julie Zhu

Last Published

February 15th, 2017

Functions in ChIPpeakAnno (2.16.4)

BED2RangedData

convert BED format to RangedData
ExonPlusUtr.human.GRCh37

Gene model with exon, 5' UTR and 3' UTR information for human sapiens (GRCh37) obtained from biomaRt
myPeakList

ChIP-seq peak dataset
findOverlappingPeaks

Find the overlapping peaks for two peak ranges.
Peaks.Ste12.Replicate1

Ste12-binding sites from biological replicate 1 in yeast (see reference)
TSS.zebrafish.Zv9

TSS annotation for Danio rerio (Zv9) obtained from biomaRt
annotatePeakInBatch

obtain the distance to the nearest TSS, miRNA, exon et al for a list of peak intervals
findVennCounts

Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram
annotatedPeak

Annotated Peaks
getAllPeakSequence

Obtain genomic sequences around the peaks
hyperGtest

hypergeometric test
getEnrichedPATH

Obtain enriched PATH that near the peaks
peaksNearBDP

obtain the peaks near bi-directional promoters
getGeneSeq

get gene sequence using biomaRt package
TSS.rat.Rnor_5.0

TSS annotation data for Rattus norvegicus (Rnor_5.0) obtained from biomaRt
summarizePatternInPeaks

Output a summary of the occurrence of each pattern in the sequences.
TSS.zebrafish.Zv8

TSS annotation data for zebrafish (Zv8) obtained from biomaRt
convert2EntrezID

Convert other common IDs such as ensemble gene id, gene symbol, refseq id to entrez gene ID.
condenseMatrixByColnames

condense matrix by colnames
write2FASTA

write sequences to a file in fasta format
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.
getAnnotation

Obtain the TSS, exon or miRNA annotation for the specified species
TSS.mouse.GRCm38

TSS annotation data for Mus musculus (GRCm38.p1) obtained from biomaRt
TSS.human.NCBI36

TSS annotation for human sapiens (NCBI36) obtained from biomaRt
makeVennDiagram

Make Venn Diagram from two peak ranges
getEnrichedGO

Obtain enriched gene ontology (GO) terms that near the peaks
Peaks.Ste12.Replicate3

Ste12-binding sites from biological replicate 3 in yeast (see reference)
Peaks.Ste12.Replicate2

Ste12-binding sites from biological replicate 2 in yeast (see reference)
getUniqueGOidCount

get the count for each unique GO ID
ChIPpeakAnno-package

Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.
TSS.human.GRCh37

TSS annotation for human sapiens (GRCh37) obtained from biomaRt
GFF2RangedData

convert GFF format to RangedData
translatePattern

translate pattern from IUPAC Extended Genetic Alphabet to regular expression
TSS.mouse.NCBIM37

TSS annotation data for mouse (NCBIM37) obtained from biomaRt
countPatternInSeqs

Output total number of patterns found in the input sequences
enrichedGO

Enriched Gene Ontology terms used as example
TSS.rat.RGSC3.4

TSS annotation data for rat (RGSC3.4) obtained from biomaRt