Package: ChIPpeakAnno 3.39.1

Jianhong Ou

ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

The package encompasses a range of functions for identifying the closest gene, exon, miRNA, or custom features—such as highly conserved elements and user-supplied transcription factor binding sites. Additionally, users can retrieve sequences around the peaks and obtain enriched Gene Ontology (GO) or Pathway terms. In version 2.0.5 and beyond, new functionalities have been introduced. These include features for identifying peaks associated with bi-directional promoters along with summary statistics (peaksNearBDP), summarizing motif occurrences in peaks (summarizePatternInPeaks), and associating additional identifiers with annotated peaks or enrichedGO (addGeneIDs). The package integrates with various other packages such as biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and stat to enhance its analytical capabilities.

Authors:Lihua Julie Zhu, Jianhong Ou, Jun Yu, Kai Hu, Haibo Liu, Junhui Li, Hervé Pagès, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe, Michael Green

ChIPpeakAnno_3.39.1.tar.gz
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ChIPpeakAnno.pdf |ChIPpeakAnno.html✨
ChIPpeakAnno/json (API)
NEWS

# Install 'ChIPpeakAnno' in R:
install.packages('ChIPpeakAnno', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • ExonPlusUtr.human.GRCh37 - Gene model with exon, 5' UTR and 3' UTR information for human sapiens (GRCh37) obtained from biomaRt
  • HOT.spots - High Occupancy of Transcription Related Factors regions
  • Peaks.Ste12.Replicate1 - Ste12-binding sites from biological replicate 1 in yeast
  • Peaks.Ste12.Replicate2 - Ste12-binding sites from biological replicate 2 in yeast
  • Peaks.Ste12.Replicate3 - Ste12-binding sites from biological replicate 3 in yeast
  • TSS.human.GRCh37 - TSS annotation for human sapiens (GRCh37) obtained from biomaRt
  • TSS.human.GRCh38 - TSS annotation for human sapiens (GRCh38) obtained from biomaRt
  • 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
  • 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 from biomaRt
  • TSS.zebrafish.Zv8 - TSS annotation data for zebrafish (Zv8) obtained from biomaRt
  • TSS.zebrafish.Zv9 - TSS annotation for Danio rerio (Zv9) obtained from biomaRt
  • annotatedPeak - Annotated Peaks
  • enrichedGO - Enriched Gene Ontology terms used as example
  • myPeakList - An example GRanges object representing a ChIP-seq peak dataset
  • peaks1 - An example GRanges object representing a ChIP-seq peak dataset
  • peaks2 - An example GRanges object representing a ChIP-seq peak dataset
  • peaks3 - An example GRanges object representing a ChIP-seq peak dataset
  • wgEncodeTfbsV3 - Transcription factor binding site clusters (V3) from ENCODE

On BioConductor:ChIPpeakAnno-3.39.0(bioc 3.20)ChIPpeakAnno-3.38.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

59 exports 6.40 score 122 dependencies 6 dependents 145 mentions

Last updated 7 days agofrom:b0405a13b7

Exports:addAncestorsaddGeneIDsaddMetadataannoGRannoPeaksannotatePeakInBatchassignChromosomeRegionbinOverFeaturebinOverGenebinOverRegionscoercecondenseMatrixByColnamesconvert2EntrezIDcountPatternInSeqscumulativePercentagedownstreamsegOrgMapenrichmentPlotestFragmentLengthestLibSizefeatureAlignedDistributionfeatureAlignedExtendSignalfeatureAlignedHeatmapfeatureAlignedSignalfindEnhancersfindMotifsInPromoterSeqsfindOverlappingPeaksfindOverlapsOfPeaksgenomicElementDistributiongenomicElementUpSetRgetAllPeakSequencegetAnnotationgetEnrichedGOgetEnrichedPATHgetGOgetUniqueGOidCountgetVennCountshyperGtestIDRfilterinfomakeVennDiagrammergePlusMinusPeaksmetagenePlotoligoFrequencyoligoSummarypeakPermTestpeaksNearBDPpie1plotBinOverRegionspreparePoolreCenterPeakssummarizeOverlapsByBinssummarizePatternInPeakstileCounttileGRangestoGRangestranslatePatternwrite2FASTAxget

Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdplyrensembldbfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegraphgtablehmshttrhttr2InteractionSetIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemulttestmunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogressProtGenericspurrrpwalignR6rappdirsRBGLRColorBrewerRcppRcppThreadRCurlregioneRrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsuniversalmotifutf8vctrsVennDiagramviridisLitewithrXMLxml2XVectoryamlzlibbioc

ChIPpeakAnno: annotate, visualize, and compare peak data

Jianhong Ou, Kai Hu, Haibo Liu, Junhui Li, Jun Yu, Lihua Julie Zhu

Rendered fromChIPpeakAnno.Rmdusingknitr::rmarkdownon Jul 04 2024.

Last update: 2024-01-24
Started: 2015-10-07

Readme and manuals

Help Manual

Help pageTopics
Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.ChIPpeakAnno-package ChIPpeakAnno
Add GO IDs of the ancestors for a given vector of GO idsaddAncestors
Add common IDs to annotated peaks such as gene symbol, entrez ID, ensemble gene id and refseq id.addGeneIDs
Add metadata of the GRanges objects used for findOverlapsOfPeaksaddMetadata
Class 'annoGR'annoGR annoGR,EnsDb-method annoGR,GRanges-method annoGR,TxDb-method annoGR-class coerce coerce,annoGR,GRanges-method coerce,GRanges,annoGR-method info info,annoGR-method
Annotate peaksannoPeaks
Annotated PeaksannotatedPeak
Obtain the distance to the nearest TSS, miRNA, and/or exon for a list of peaksannotatePeakInBatch
Summarize peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTRassignChromosomeRegion
obtain the peaks near bi-directional promotersbdp
Class '"bindist"'$,bindist-method $<-,bindist-method bindist bindist-class bindist-method
Aggregate peaks over bins from the TSSbinOverFeature
coverage of gene bodybinOverGene
coverage of chromosome regionsbinOverRegions
Deprecated Functions in Package ChIPpeakAnnoChIPpeakAnno-deprecated
count overlapscntOverlaps
Condense matrix by colnamescondenseMatrixByColnames
Convert other common IDs to entrez gene ID.convert2EntrezID
Output total number of patterns found in the input sequencescountPatternInSeqs
Plot the cumulative percentage tag allocation in samplecumulativePercentage
Get downstream coordinatesdownstreams
Convert between the name of the organism annotation package ("OrgDb") and the name of the organism.egOrgMap
Enriched Gene Ontology terms used as exampleenrichedGO
plot enrichment resultsenrichmentPlot
EnsDb object to GRangesEnsDb2GR
estimate the fragment lengthestFragmentLength
estimate the library sizeestLibSize
Gene model with exon, 5' UTR and 3' UTR information for human sapiens (GRCh37) obtained from biomaRtExonPlusUtr.human.GRCh37
plot distribution in given rangesfeatureAlignedDistribution
extract signals in given ranges from bam filesfeatureAlignedExtendSignal
Heatmap representing signals in given rangesfeatureAlignedHeatmap
extract signals in given rangesfeatureAlignedSignal
Find possible enhancers depend on DNA interaction datafindEnhancers
Find occurence of input motifs in the promoter regions of the input gene listfindMotifsInPromoterSeqs
Find the overlapping peaks for two peak ranges.findOverlappingPeaks findOverlappingPeaks-deprecated
Find the overlapped peaks among two or more set of peaks.findOverlapsOfPeaks overlappingPeaks overlappingPeaks-class
Genomic Element distributiongenomicElementDistribution
Genomic Element data for upset plotgenomicElementUpSetR
Obtain genomic sequences around the peaksgetAllPeakSequence
Obtain the TSS, exon or miRNA annotation for the specified speciesgetAnnotation
Obtain enriched gene ontology (GO) terms that near the peaksgetEnrichedGO
Obtain enriched PATH that near the peaksgetEnrichedPATH
Obtain gene ontology (GO) terms for given genesgetGO
Obtain Venn Counts for Venn Diagram, internal function for makeVennDigramgetVennCounts
High Occupancy of Transcription Related Factors regionsHOT.spots
Filter peaks by IDR (irreproducible discovery rate)IDRfilter
Make Venn Diagram from a list of peaksmakeVennDiagram
Merge peaks from plus strand and minus strandmergePlusMinusPeaks
peak distance to featuresmetagenePlot
An example GRanges object representing a ChIP-seq peak datasetmyPeakList
get the oligonucleotide frequencyoligoFrequency
Output a summary of consensus in the peaksoligoSummary
Permutation Test for two given peak listspeakPermTest
Ste12-binding sites from biological replicate 1 in yeast (see reference)Peaks.Ste12.Replicate1
Ste12-binding sites from biological replicate 2 in yeast (see reference)Peaks.Ste12.Replicate2
Ste12-binding sites from biological replicate 3 in yeast (see reference)Peaks.Ste12.Replicate3
An example GRanges object representing a ChIP-seq peak datasetpeaks1
An example GRanges object representing a ChIP-seq peak datasetpeaks2
An example GRanges object representing a ChIP-seq peak datasetpeaks3
obtain the peaks near bi-directional promoterspeaksNearBDP
Class '"permPool"'$,permPool-method $<-,permPool-method permPool permPool-class permPool-method
Pie Chartspie1
plot the coverage of regionsplotBinOverRegions
prepare data for permutation testpreparePool
re-center the peaksreCenterPeaks
Perform overlap queries between reads and genomic features by binssummarizeOverlapsByBins
Output a summary of the occurrence and enrichment of each pattern in the sequences.summarizePatternInPeaks
Perform overlap queries between reads and genome by windowstileCount
Slide windows on a given GRanges objecttileGRanges
Convert dataset to GRangestoGRanges toGRanges,character-method toGRanges,connection-method toGRanges,data.frame-method toGRanges,EnsDb-method toGRanges,TxDb-method
translate pattern from IUPAC Extended Genetic Alphabet to regular expressiontranslatePattern
TSS annotation for human sapiens (GRCh37) obtained from biomaRtTSS.human.GRCh37
TSS annotation for human sapiens (GRCh38) obtained from biomaRtTSS.human.GRCh38
TSS annotation for human sapiens (NCBI36) obtained from biomaRtTSS.human.NCBI36
TSS annotation data for Mus musculus (GRCm38.p1) obtained from biomaRtTSS.mouse.GRCm38
TSS annotation data for mouse (NCBIM37) obtained from biomaRtTSS.mouse.NCBIM37
TSS annotation data for rat (RGSC3.4) obtained from biomaRtTSS.rat.RGSC3.4
TSS annotation data for Rattus norvegicus (Rnor_5.0) obtained from biomaRtTSS.rat.Rnor_5.0
TSS annotation data for zebrafish (Zv8) obtained from biomaRtTSS.zebrafish.Zv8
TSS annotation for Danio rerio (Zv9) obtained from biomaRtTSS.zebrafish.Zv9
TxDb object to GRangesTxDb2GR
transcription factor binding site clusters (V3) from ENCODEwgEncodeTfbsV3
Write sequences to a file in fasta formatwrite2FASTA
Return the value from a Bimap objectsxget