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.

Author
Lihua Julie Zhu, Jianhong Ou, Jun Yu, Herve Pages, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe and Michael Green
Date of publication
None
Maintainer
Lihua Julie Zhu <julie.zhu@umassmed.edu>, Jianhong Ou <Jianhong.ou@umassmed.edu>
License
GPL (>= 2)
Version
3.8.2

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
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

Files in this package

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