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ChIPpeakAnno (version 3.4.0)

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

3.4.0

License

GPL (>= 2)

Maintainer

Lihua Julie Zhu

Last Published

February 15th, 2017

Functions in ChIPpeakAnno (3.4.0)

annotatePeakInBatch

Obtain the distance to the nearest TSS, miRNA, and/or exon for a list of peaks
convert2EntrezID

Convert other common IDs to entrez gene ID.
countPatternInSeqs

Output total number of patterns found in the input sequences
getUniqueGOidCount

get the count for each unique GO ID
peakPermTest

Permutation Test for two given peak lists
getVennCounts

Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram
Peaks.Ste12.Replicate1

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

Summarize peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR
TSS.rat.Rnor_5.0

TSS annotation data for Rattus norvegicus (Rnor_5.0) obtained from biomaRt
TSS.rat.RGSC3.4

TSS annotation data for rat (RGSC3.4) obtained from biomaRt
BED2RangedData

Convert BED format to RangedData
bindist-class

Class "bindist"
featureAlignedHeatmap

Heatmap representing signals in given ranges
featureAlignedSignal

extract signals in given ranges
ChIPpeakAnno-package

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

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

Find the overlapping peaks for two peak ranges.
translatePattern

translate pattern from IUPAC Extended Genetic Alphabet to regular expression
condenseMatrixByColnames

Condense matrix by colnames
getEnrichedGO

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

hypergeometric test
getAnnotation

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

Make Venn Diagram from a list of peaks
TSS.human.GRCh37

TSS annotation for human sapiens (GRCh37) obtained from biomaRt
ChIPpeakAnno-deprecated

Deprecated Functions in Package ChIPpeakAnno
egOrgMap

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

Aggregate peaks over bins from the TSS
enrichedGO

Enriched Gene Ontology terms used as example
getEnrichedPATH

Obtain enriched PATH that near the peaks
getGeneSeq

Get gene sequence using the biomaRt package
GFF2RangedData

Convert GFF format to RangedData
HOT.spots

High Occupancy of Transcription Related Factors regions
summarizePatternInPeaks

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

Convert dataset to GRanges
preparePool

prepare data for permutation test
pie1

Pie Charts
wgEncodeTfbsV3

transcription factor binding site clusters (V3) from ENCODE
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.
ExonPlusUtr.human.GRCh37

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

Merge peaks from plus strand and minus strand
featureAlignedDistribution

plot distribution in given ranges
myPeakList

An example GRanges object representing a ChIP-seq peak dataset
permPool-class

Class "permPool"
peaksNearBDP

obtain the peaks near bi-directional promoters
TSS.zebrafish.Zv8

TSS annotation data for zebrafish (Zv8) obtained from biomaRt
TSS.zebrafish.Zv9

TSS annotation for Danio rerio (Zv9) obtained from biomaRt
annoGR-class

Class annoGR
findVennCounts

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

Annotated Peaks
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.GRCh38

TSS annotation for human sapiens (GRCh38) obtained from biomaRt
TSS.human.NCBI36

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

Obtain genomic sequences around the peaks
TSS.mouse.NCBIM37

TSS annotation data for mouse (NCBIM37) obtained from biomaRt
TSS.mouse.GRCm38

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