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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPpeakAnno")
AuthorLihua Julie Zhu, Jianhong Ou, Jun Yu, Herve Pages, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe and Michael Green
Bioconductor views Annotation ChIPSeq ChIPchip
Date of publicationNone
MaintainerLihua Julie Zhu <julie.zhu@umassmed.edu>, Jianhong Ou <Jianhong.ou@umassmed.edu>
LicenseGPL (>= 2)
Version3.10.1

View on Bioconductor

Man pages

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...

addMetadata: Add metadata of the GRanges objects used for...

annoGR: Class 'annoGR'

annoPeaks: Annotate peaks

annotatedPeak: Annotated Peaks

annotatePeakInBatch: Obtain the distance to the nearest TSS, miRNA, and/or exon...

assignChromosomeRegion: Summarize peak distribution over exon, intron, enhancer,...

bdp: obtain the peaks near bi-directional promoters

BED2RangedData: Convert BED format to RangedData

bindist: Class '"bindist"'

binOverFeature: Aggregate peaks over bins from the TSS

ChIPpeakAnno-deprecated: Deprecated Functions in Package ChIPpeakAnno

ChIPpeakAnno-package: Batch annotation of the peaks identified from either ChIP-seq...

condenseMatrixByColnames: Condense matrix by colnames

convert2EntrezID: Convert other common IDs to entrez gene ID.

countPatternInSeqs: Output total number of patterns found in the input sequences

cumulativePercentage: Plot the cumulative percentage tag allocation in sample

egOrgMap: Convert between the name of the organism annotation package...

enrichedGO: Enriched Gene Ontology terms used as example

estFragmentLength: estimate the fragment length

estLibSize: estimate the library size

ExonPlusUtr.human.GRCh37: Gene model with exon, 5' UTR and 3' UTR information for human...

featureAlignedDistribution: plot distribution in given ranges

featureAlignedExtentSignal: extract signals in given ranges from bam files

featureAlignedHeatmap: Heatmap representing signals in given ranges

featureAlignedSignal: extract signals in given ranges

findEnhancers: Find possible enhancers depend on DNA interaction data

findOverlappingPeaks: Find the overlapping peaks for two peak ranges.

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

findVennCounts: Obtain Venn Counts for Venn Diagram, internal function for...

getAllPeakSequence: Obtain genomic sequences around the peaks

getAnnotation: Obtain the TSS, exon or miRNA annotation for the specified...

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

getEnrichedPATH: Obtain enriched PATH that near the peaks

getGeneSeq: Get gene sequence using the biomaRt package

getUniqueGOidCount: get the count for each unique GO ID

getVennCounts: Obtain Venn Counts for Venn Diagram, internal function for...

GFF2RangedData: Convert GFF format to RangedData

HOT.spots: High Occupancy of Transcription Related Factors regions

hyperGtest: hypergeometric test

IDRfilter: Filter peaks by IDR (irreproducible discovery rate)

makeVennDiagram: Make Venn Diagram from a list of peaks

mergePlusMinusPeaks: Merge peaks from plus strand and minus strand

myPeakList: An example GRanges object representing a ChIP-seq peak...

oligoFrequency: get the oligonucleotide frequency

oligoSummary: Output a summary of consensus in the peaks

peakPermTest: Permutation Test for two given peak lists

peaksNearBDP: obtain the peaks near bi-directional promoters

Peaks.Ste12.Replicate1: Ste12-binding sites from biological replicate 1 in yeast (see...

Peaks.Ste12.Replicate2: Ste12-binding sites from biological replicate 2 in yeast (see...

Peaks.Ste12.Replicate3: Ste12-binding sites from biological replicate 3 in yeast (see...

permPool: Class '"permPool"'

pie1: Pie Charts

preparePool: prepare data for permutation test

reCenterPeaks: re-center the peaks

summarizeOverlapsByBins: Perform overlap queries between reads and genomic features by...

summarizePatternInPeaks: Output a summary of the occurrence of each pattern in the...

tileCount: Perform overlap queries between reads and genome by windows

tileGRanges: Slide windows on a given GRanges object

toGRanges: Convert dataset to GRanges

translatePattern: translate pattern from IUPAC Extended Genetic Alphabet to...

TSS.human.GRCh37: TSS annotation for human sapiens (GRCh37) obtained from...

TSS.human.GRCh38: TSS annotation for human sapiens (GRCh38) obtained from...

TSS.human.NCBI36: TSS annotation for human sapiens (NCBI36) obtained from...

TSS.mouse.GRCm38: TSS annotation data for Mus musculus (GRCm38.p1) obtained...

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.rat.Rnor_5.0: TSS annotation data for Rattus norvegicus (Rnor_5.0) obtained...

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

TSS.zebrafish.Zv9: TSS annotation for Danio rerio (Zv9) obtained from biomaRt

wgEncodeTfbsV3: transcription factor binding site clusters (V3) from ENCODE

write2FASTA: Write sequences to a file in fasta format

xget: Return the value from a Bimap objects

Functions

addAncestors Man page
addGeneIDs Man page
addMetadata Man page
annoGR Man page
annoGR-class Man page
annoGR,EnsDb-method Man page
annoGR,GRanges-method Man page
annoGR,TxDb-method Man page
annoPeaks Man page
annotatedPeak Man page
annotatePeakInBatch Man page
assignChromosomeRegion Man page
bdp Man page
BED2RangedData Man page
BED2RangedData-deprecated Man page
bindist Man page
bindist-class Man page
$<-,bindist-method Man page
$,bindist-method Man page
bindist-method Man page
binOverFeature Man page
ChIPpeakAnno Man page
ChIPpeakAnno-deprecated Man page
ChIPpeakAnno-package Man page
coerce,annoGR,GRanges-method Man page
coerce,GRanges,annoGR-method Man page
condenseMatrixByColnames Man page
convert2EntrezID Man page
countPatternInSeqs Man page
cumulativePercentage Man page
egOrgMap Man page
enrichedGO Man page
estFragmentLength Man page
estLibSize Man page
ExonPlusUtr.human.GRCh37 Man page
featureAlignedDistribution Man page
featureAlignedExtendSignal Man page
featureAlignedHeatmap Man page
featureAlignedSignal Man page
findEnhancers Man page
findOverlappingPeaks Man page
findOverlappingPeaks-deprecated Man page
findOverlapsOfPeaks Man page
findVennCounts Man page
getAllPeakSequence Man page
getAnnotation Man page
getEnrichedGO Man page
getEnrichedPATH Man page
getGeneSeq Man page
getUniqueGOidCount Man page
getVennCounts Man page
GFF2RangedData Man page
GFF2RangedData-deprecated Man page
HOT.spots Man page
hyperGtest Man page
IDRfilter Man page
info Man page
info,annoGR-method Man page
makeVennDiagram Man page
mergePlusMinusPeaks Man page
myPeakList Man page
oligoFrequency Man page
oligoSummary Man page
overlappingPeaks Man page
overlappingPeaks-class Man page
peakPermTest Man page
peaksNearBDP Man page
Peaks.Ste12.Replicate1 Man page
Peaks.Ste12.Replicate2 Man page
Peaks.Ste12.Replicate3 Man page
permPool Man page
permPool-class Man page
$<-,permPool-method Man page
$,permPool-method Man page
permPool-method Man page
pie1 Man page
preparePool Man page
reCenterPeaks Man page
summarizeOverlapsByBins Man page
summarizePatternInPeaks Man page
tileCount Man page
tileGRanges Man page
toGRanges Man page
toGRanges,character-method Man page
toGRanges,connection-method Man page
toGRanges,data.frame-method Man page
toGRanges,EnsDb-method Man page
toGRanges,RangedData-method Man page
toGRanges,TxDb-method Man page
translatePattern Man page
TSS.human.GRCh37 Man page
TSS.human.GRCh38 Man page
TSS.human.NCBI36 Man page
TSS.mouse.GRCm38 Man page
TSS.mouse.NCBIM37 Man page
TSS.rat.RGSC3.4 Man page
TSS.rat.Rnor_5.0 Man page
TSS.zebrafish.Zv8 Man page
TSS.zebrafish.Zv9 Man page
wgEncodeTfbsV3 Man page
write2FASTA Man page
xget Man page

Files

DESCRIPTION
NAMESPACE
R
R/BED2RangedData.R R/GFF2RangedData.R R/IDRfilter.R R/addAncestors.R R/addGeneIDs.R R/addMetadata.R R/annoGR.R R/annoPeaks.R R/annotatePeakInBatch.R R/assignChromosomeRegion.R R/bdp.R R/binOverFeature.R R/bindist.R R/buildBindingDistribution.R R/cntOverlaps.R R/condenseMatrixByColnames.R R/convert2EntrezID.R R/countPatternInSeqs.R R/cumulativePercentage.R R/egOrgMap.R R/estFragmentLength.R R/estLibSize.R R/expandGR.R R/featureAlignedDistribution.R R/featureAlignedExtendSignal.R R/featureAlignedHeatmap.R R/featureAlignedSignal.R R/findEnhancers.R R/findOverlappingPeaks.R R/findOverlapsOfPeaks.R R/findVennCounts.R R/getAllPeakSequence.R R/getAnnotation.R R/getEnrichedGO.R R/getEnrichedPATH.R R/getGeneSeq.R R/getUniqueGOidCount.R R/getVennCounts.R R/hyperGtest.R R/makeVennDiagram.R R/mergePlusMinusPeaks.R R/oligoSummary.R R/peakPermTest.R R/peaksNearBDP.R R/permPool.R R/pie1.R R/preparePool.R R/privateUtil.R R/randPeaks.R R/ratio.zScore.R R/reCenterPeaks.R R/summarizeOverlapsByBins.R R/summarizePatternInPeaks.R R/tileCount.R R/tileGRanges.R R/toGRanges.R R/translatePattern.R R/write2FASTA.R R/xget.R
build
build/vignette.rds
data
data/ExonPlusUtr.human.GRCh37.rda
data/HOT.spots.rda
data/Peaks.Ste12.Replicate1.rda
data/Peaks.Ste12.Replicate2.rda
data/Peaks.Ste12.Replicate3.rda
data/TSS.human.GRCh37.rda
data/TSS.human.GRCh38.rda
data/TSS.human.NCBI36.rda
data/TSS.mouse.GRCm38.rda
data/TSS.mouse.NCBIM37.rda
data/TSS.rat.RGSC3.4.rda
data/TSS.rat.Rnor_5.0.rda
data/TSS.zebrafish.Zv8.rda
data/TSS.zebrafish.Zv9.rda
data/annotatedPeak.rda
data/datalist
data/enrichedGO.rda
data/myPeakList.rda
data/wgEncodeTfbsV3.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/ChIPpeakAnno.R
inst/doc/ChIPpeakAnno.Rmd
inst/doc/ChIPpeakAnno.html
inst/doc/FAQs.R
inst/doc/FAQs.Rmd
inst/doc/FAQs.html
inst/doc/pipeline.R
inst/doc/pipeline.Rmd
inst/doc/pipeline.html
inst/doc/quickStart.R
inst/doc/quickStart.Rmd
inst/doc/quickStart.html
inst/extdata
inst/extdata/GFF_peaks.gff
inst/extdata/GSM700906_AA86_vs_INPUT_WS170.bed
inst/extdata/GSM700907_DAF-12_TAP_vs_INPUT_#1_WS170.bed
inst/extdata/GSM700908_DAF-12_TAP_vs_INPUT_#2_WS170.bed
inst/extdata/GSM700909_DAF-12_TAP_vs_INPUT_#3_WS170.bed
inst/extdata/MACS2_peaks.xls
inst/extdata/MACS_output.bed
inst/extdata/MACS_peaks.xls
inst/extdata/TAF.bigWig
inst/extdata/TAF.broadPeak
inst/extdata/Tead4.bigWig
inst/extdata/Tead4.broadPeak
inst/extdata/WS220.bed
inst/extdata/YY1.bigWig
inst/extdata/YY1.broadPeak
inst/extdata/annotatedPeaks.2.10.0.rds
inst/extdata/cvglist.rds
inst/extdata/examplePattern.fa
inst/extdata/gadem.rda
inst/extdata/guide-seq-peaks.txt
inst/extdata/peaks.narrowPeak
inst/extdata/peaks_hg19.bed
inst/extdata/ref.gtf
inst/extdata/test.bed
inst/extdata/wgEncodeUmassDekker5CGm12878PkV2.bed.gz
man
man/BED2RangedData.Rd man/ChIPpeakAnno-deprecated.Rd man/ChIPpeakAnno-package.Rd man/ExonPlusUtr.human.GRCh37.Rd man/GFF2RangedData.Rd man/HOT.spots.Rd man/IDRfilter.Rd man/Peaks.Ste12.Replicate1.Rd man/Peaks.Ste12.Replicate2.Rd man/Peaks.Ste12.Replicate3.Rd man/TSS.human.GRCh37.Rd man/TSS.human.GRCh38.Rd man/TSS.human.NCBI36.Rd man/TSS.mouse.GRCm38.Rd man/TSS.mouse.NCBIM37.Rd man/TSS.rat.RGSC3.4.Rd man/TSS.rat.Rnor_5.0.Rd man/TSS.zebrafish.Zv8.Rd man/TSS.zebrafish.Zv9.Rd man/addAncestors.Rd man/addGeneIDs.Rd man/addMetadata.Rd man/annoGR.Rd man/annoPeaks.Rd man/annotatePeakInBatch.Rd man/annotatedPeak.Rd man/assignChromosomeRegion.Rd man/bdp.Rd man/binOverFeature.Rd man/bindist.Rd man/condenseMatrixByColnames.Rd man/convert2EntrezID.Rd man/countPatternInSeqs.Rd man/cumulativePercentage.Rd man/egOrgMap.Rd man/enrichedGO.Rd man/estFragmentLength.Rd man/estLibSize.Rd man/featureAlignedDistribution.Rd man/featureAlignedExtentSignal.Rd man/featureAlignedHeatmap.Rd man/featureAlignedSignal.Rd man/findEnhancers.Rd man/findOverlappingPeaks.Rd man/findOverlapsOfPeaks.Rd man/findVennCounts.Rd man/getAllPeakSequence.Rd man/getAnnotation.Rd man/getEnrichedGO.Rd man/getEnrichedPATH.Rd man/getGeneSeq.Rd man/getUniqueGOidCount.Rd man/getVennCounts.Rd man/hyperGtest.Rd man/makeVennDiagram.Rd man/mergePlusMinusPeaks.Rd man/myPeakList.Rd man/oligoFrequency.Rd man/oligoSummary.Rd man/peakPermTest.Rd man/peaksNearBDP.Rd man/permPool.Rd man/pie1.Rd man/preparePool.Rd man/reCenterPeaks.Rd man/summarizeOverlapsByBins.Rd man/summarizePatternInPeaks.Rd man/tileCount.Rd man/tileGRanges.Rd man/toGRanges.Rd man/translatePattern.Rd man/wgEncodeTfbsV3.Rd man/write2FASTA.Rd man/xget.Rd
tests
tests/runTests.R
tests/testthat
tests/testthat/test_addGeneIDs.R tests/testthat/test_addMetadata.R tests/testthat/test_annoPeaks.R tests/testthat/test_annotatePeakInBatch.R tests/testthat/test_assignChromosomeRegion.R tests/testthat/test_bdp.R tests/testthat/test_binOverFeature.R tests/testthat/test_feature.R tests/testthat/test_findEnhancers.R tests/testthat/test_findOverlapsOfPeaks.R tests/testthat/test_getAllPeakSequence.R tests/testthat/test_getAnnotation.R tests/testthat/test_getVennCounts.R tests/testthat/test_makeVennDiagram.R tests/testthat/test_peaksNearBDP.R tests/testthat/test_reCenterPeaks.R tests/testthat/test_toGRanges.R tests/testthat/test_write2FASTA.R
vignettes
vignettes/ChIPpeakAnno.Rmd
vignettes/FAQs.Rmd
vignettes/bibliography.bib
vignettes/custom.css
vignettes/nature.csl
vignettes/pipeline.Rmd
vignettes/quickStart.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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