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ChIPpeakAnno (version 3.6.4)

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

3.6.4

License

GPL (>= 2)

Maintainer

Lihua Julie Zhu

Last Published

February 15th, 2017

Functions in ChIPpeakAnno (3.6.4)

assignChromosomeRegion

Summarize peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR

TSS.mouse.NCBIM37

TSS annotation data for mouse (NCBIM37) obtained from biomaRt

featureAlignedSignal

extract signals in given ranges

getAllPeakSequence

Obtain genomic sequences around the peaks

getUniqueGOidCount

get the count for each unique GO ID

condenseMatrixByColnames

Condense matrix by colnames

Convert dataset to GRanges

re-center the peaks

annotatePeakInBatch

Obtain the distance to the nearest TSS, miRNA, and/or exon for a list of peaks

obtain the peaks near bi-directional promoters

Obtain the TSS, exon or miRNA annotation for the specified species

findOverlappingPeaks

Find the overlapping peaks for two peak ranges.

Enriched Gene Ontology terms used as example

Add metadata of the GRanges objects used for findOverlapsOfPeaks

findOverlapsOfPeaks

Find the overlapped peaks among two or more set of peaks.

Peaks.Ste12.Replicate3

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

Convert GFF format to RangedData

translatePattern

translate pattern from IUPAC Extended Genetic Alphabet to regular expression

Add GO IDs of the ancestors for a given vector of GO ids

ExonPlusUtr.human.GRCh37

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

Peaks.Ste12.Replicate1

Ste12-binding sites from biological replicate 1 in yeast (see reference)

ChIPpeakAnno-package

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

makeVennDiagram

Make Venn Diagram from a list of peaks

Class "bindist"

Annotated Peaks

convert2EntrezID

Convert other common IDs to entrez gene ID.

prepare data for permutation test

hypergeometric test

Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram

Permutation Test for two given peak lists

summarizePatternInPeaks

Output a summary of the occurrence of each pattern in the sequences.

obtain the peaks near bi-directional promoters

Output a summary of consensus in the peaks

Return the value from a Bimap objects

ChIPpeakAnno-deprecated

Deprecated Functions in Package ChIPpeakAnno

featureAlignedDistribution

plot distribution in given ranges

Get gene sequence using the biomaRt package

Write sequences to a file in fasta format

featureAlignedHeatmap

Heatmap representing signals in given ranges

TSS.rat.RGSC3.4

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

Class "permPool"

Convert BED format to RangedData

Peaks.Ste12.Replicate2

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

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

Aggregate peaks over bins from the TSS

Convert between the name of the organism annotation package ("OrgDb") and the name of the organism.

countPatternInSeqs

Output total number of patterns found in the input sequences

Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram

mergePlusMinusPeaks

Merge peaks from plus strand and minus strand

Filter peaks by IDR (irreproducible discovery rate)

TSS.human.GRCh38

TSS annotation for human sapiens (GRCh38) obtained from biomaRt

TSS.rat.Rnor_5.0

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

TSS.zebrafish.Zv9

TSS annotation for Danio rerio (Zv9) obtained from biomaRt

Obtain enriched gene ontology (GO) terms that near the peaks

summarizeOverlapsByBins

Perform overlap queries between reads and genomic features by bins

getEnrichedPATH

Obtain enriched PATH that near the peaks

transcription factor binding site clusters (V3) from ENCODE

An example GRanges object representing a ChIP-seq peak dataset

Find possible enhancers depend on DNA interaction data

High Occupancy of Transcription Related Factors regions

TSS.human.GRCh37

TSS annotation for human sapiens (GRCh37) obtained from biomaRt

Add common IDs to annotated peaks such as gene symbol, entrez ID, ensemble gene id and refseq id.

TSS.zebrafish.Zv8

TSS annotation data for zebrafish (Zv8) obtained from biomaRt

get the oligonucleotide frequency