{ "_id": "6a1ae8511d7bb097a09f1b13", "Package": "ChIPpeakAnno", "Type": "Package", "Title": "Batch annotation of the peaks identified from either ChIP-seq,\nChIP-chip experiments, or any experiments that result in large\nnumber of genomic interval data", "Version": "3.46.0", "Encoding": "UTF-8", "Author": "Lihua Julie Zhu, Jianhong Ou, Jun Yu, Kai Hu, Haibo Liu, Junhui\nLi, Hervé Pagès, Claude Gazin, Nathan Lawson, Ryan Thompson,\nSimon Lin, David Lapointe, Michael Green", "Maintainer": "Jianhong Ou , Lihua Julie Zhu\n, Kai Hu , Junhui\nLi ", "Description": "The package encompasses a range of functions for\nidentifying the closest gene, exon, miRNA, or custom\nfeatures—such as highly conserved elements and user-supplied\ntranscription factor binding sites. Additionally, users can\nretrieve sequences around the peaks and obtain enriched Gene\nOntology (GO) or Pathway terms. In version 2.0.5 and beyond,\nnew functionalities have been introduced. These include\nfeatures for identifying peaks associated with bi-directional\npromoters along with summary statistics (peaksNearBDP),\nsummarizing motif occurrences in peaks\n(summarizePatternInPeaks), and associating additional\nidentifiers with annotated peaks or enrichedGO (addGeneIDs).\nThe package integrates with various other packages such as\nbiomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and\nstat to enhance its analytical capabilities.", "License": "GPL (>= 2)", "LazyLoad": "yes", "LazyData": "true", "LazyDataCompression": "xz", "biocViews": "Annotation, ChIPSeq, ChIPchip", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:34:07 UTC", "RemoteUrl": "https://github.com/bioc/ChIPpeakAnno", "RemoteRef": "RELEASE_3_23", "RemoteSha": 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"title": "Add GO IDs of the ancestors for a given vector of GO ids", "topics": [ "addAncestors" ] }, { "page": "addGeneIDs", "title": "Add common IDs to annotated peaks such as gene symbol, entrez ID, ensemble gene id and refseq id.", "topics": [ "addGeneIDs" ] }, { "page": "addMetadata", "title": "Add metadata of the GRanges objects used for findOverlapsOfPeaks", "topics": [ "addMetadata" ] }, { "page": "annoGR", "title": "Class 'annoGR'", "topics": [ "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" ] }, { "page": "annoPeaks", "title": "Annotate peaks", "topics": [ "annoPeaks" ] }, { "page": "annotatedPeak", "title": "Annotated Peaks", "topics": [ "annotatedPeak" ] }, { "page": "annotatePeakInBatch", "title": "Obtain the distance to the nearest TSS, miRNA, and/or exon for a list of peaks", "topics": [ "annotatePeakInBatch" ] }, { "page": 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"EnsDb2GR", "title": "EnsDb object to GRanges", "topics": [ "EnsDb2GR" ] }, { "page": "estFragmentLength", "title": "estimate the fragment length", "topics": [ "estFragmentLength" ] }, { "page": "estLibSize", "title": "estimate the library size", "topics": [ "estLibSize" ] }, { "page": "ExonPlusUtr.human.GRCh37", "title": "Gene model with exon, 5' UTR and 3' UTR information for human sapiens (GRCh37) obtained from biomaRt", "topics": [ "ExonPlusUtr.human.GRCh37" ] }, { "page": "featureAlignedDistribution", "title": "plot distribution in given ranges", "topics": [ "featureAlignedDistribution" ] }, { "page": "featureAlignedExtendSignal", "title": "extract signals in given ranges from bam files", "topics": [ "featureAlignedExtendSignal" ] }, { "page": "featureAlignedHeatmap", "title": "Heatmap representing signals in given ranges", "topics": [ "featureAlignedHeatmap" ] }, { "page": "featureAlignedSignal", "title": "extract signals in given ranges", "topics": [ "featureAlignedSignal" ] }, { "page": "findEnhancers", "title": "Find possible enhancers depend on DNA interaction data", "topics": [ "findEnhancers" ] }, { "page": "findMotifsInPromoterSeqs", "title": "Find occurence of input motifs in the promoter regions of the input gene list", "topics": [ "findMotifsInPromoterSeqs" ] }, { "page": "findOverlappingPeaks", "title": "Find the overlapping peaks for two peak ranges.", "topics": [ "findOverlappingPeaks", "findOverlappingPeaks-deprecated" ] }, { "page": "findOverlapsOfPeaks", "title": "Find the overlapped peaks among two or more set of peaks.", "topics": [ "findOverlapsOfPeaks", "overlappingPeaks", "overlappingPeaks-class" ] }, { "page": "genomicElementDistribution", "title": "Genomic Element distribution", "topics": [ "genomicElementDistribution" ] }, { "page": "genomicElementUpSetR", "title": "Genomic Element data for upset plot", "topics": [ "genomicElementUpSetR" ] }, { "page": "getAllPeakSequence", "title": "Obtain genomic sequences around the peaks", "topics": [ "getAllPeakSequence" ] }, { "page": "getAnnotation", "title": "Obtain the TSS, exon or miRNA annotation for the specified species", "topics": [ "getAnnotation" ] }, { "page": "getEnrichedGO", "title": "Obtain enriched gene ontology (GO) terms that near the peaks", "topics": [ "getEnrichedGO" ] }, { "page": "getEnrichedPATH", "title": "Obtain enriched PATH that near the peaks", "topics": [ "getEnrichedPATH" ] }, { "page": "getGO", "title": "Obtain gene ontology (GO) terms for given genes", "topics": [ "getGO" ] }, { "page": "getVennCounts", "title": "Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram", "topics": [ "getVennCounts" ] }, { "page": "HOT.spots", "title": "High Occupancy of Transcription Related Factors regions", "topics": [ "HOT.spots" ] }, { "page": "IDRfilter", "title": "Filter peaks by IDR (irreproducible discovery rate)", "topics": [ "IDRfilter" ] }, { "page": "makeVennDiagram", "title": "Make Venn Diagram from a list of peaks", "topics": [ "makeVennDiagram" ] }, { "page": "mergePlusMinusPeaks", "title": "Merge peaks from plus strand and minus strand", "topics": [ "mergePlusMinusPeaks" ] }, { "page": "metagenePlot", "title": "peak distance to features", "topics": [ "metagenePlot" ] }, { "page": "myPeakList", "title": "An example GRanges object representing a ChIP-seq peak dataset", "topics": [ "myPeakList" ] }, { "page": "oligoFrequency", "title": "get the oligonucleotide frequency", "topics": [ "oligoFrequency" ] }, { "page": "oligoSummary", "title": "Output a summary of consensus in the peaks", "topics": [ "oligoSummary" ] }, { "page": "peakPermTest", "title": "Permutation Test for two given peak lists", "topics": [ "peakPermTest" ] }, { "page": "Peaks.Ste12.Replicate1", "title": "Ste12-binding sites from biological replicate 1 in yeast (see reference)", "topics": [ "Peaks.Ste12.Replicate1" ] }, { "page": "Peaks.Ste12.Replicate2", "title": "Ste12-binding sites from biological replicate 2 in yeast (see reference)", "topics": [ "Peaks.Ste12.Replicate2" ] }, { "page": "Peaks.Ste12.Replicate3", "title": "Ste12-binding sites from biological replicate 3 in yeast (see reference)", "topics": [ "Peaks.Ste12.Replicate3" ] }, { "page": "peaks1", "title": "An example GRanges object representing a ChIP-seq peak dataset", "topics": [ "peaks1" ] }, { "page": "peaks2", "title": "An example GRanges object representing a ChIP-seq peak dataset", "topics": [ "peaks2" ] }, { "page": "peaks3", "title": "An example GRanges object representing a ChIP-seq peak dataset", "topics": [ "peaks3" ] }, { "page": "peaksNearBDP", "title": "obtain the peaks near bi-directional promoters", "topics": [ "peaksNearBDP" ] }, { "page": "permPool", "title": "Class '\"permPool\"'", "topics": [ "$,permPool-method", "$<-,permPool-method", "permPool", "permPool-class", "permPool-method" ] }, { "page": "pie1", "title": "Pie Charts", "topics": [ "pie1" ] }, { "page": "plotBinOverRegions", "title": "plot the coverage of regions", "topics": [ "plotBinOverRegions" ] }, { "page": "preparePool", "title": "prepare data for permutation test", "topics": [ "preparePool" ] }, { "page": "reCenterPeaks", "title": "re-center the peaks", "topics": [ "reCenterPeaks" ] }, { "page": "summarizeOverlapsByBins", "title": "Perform overlap queries between reads and genomic features by bins", "topics": [ "summarizeOverlapsByBins" ] }, { "page": "summarizePatternInPeaks", "title": "Output a summary of the occurrence and enrichment of each pattern in the sequences.", "topics": [ "summarizePatternInPeaks" ] }, { "page": "tileCount", "title": "Perform overlap queries between reads and genome by windows", "topics": [ "tileCount" ] }, { "page": "tileGRanges", "title": "Slide windows on a given GRanges object", "topics": [ "tileGRanges" ] }, { "page": "toGRanges", "title": "Convert dataset to GRanges", "topics": [ "toGRanges", "toGRanges,character-method", "toGRanges,connection-method", "toGRanges,data.frame-method", "toGRanges,EnsDb-method", "toGRanges,TxDb-method" ] }, { "page": "translatePattern", "title": "translate pattern from IUPAC Extended Genetic Alphabet to regular expression", "topics": [ "translatePattern" ] }, { "page": "TSS.human.GRCh37", "title": "TSS annotation for human sapiens (GRCh37) obtained from biomaRt", "topics": [ "TSS.human.GRCh37" ] }, { "page": "TSS.human.GRCh38", "title": "TSS annotation for human sapiens (GRCh38) obtained from biomaRt", "topics": [ "TSS.human.GRCh38" ] }, { "page": "TSS.human.NCBI36", "title": "TSS annotation for human sapiens (NCBI36) obtained from biomaRt", "topics": [ "TSS.human.NCBI36" ] }, { "page": "TSS.mouse.GRCm38", "title": "TSS annotation data for Mus musculus (GRCm38.p1) obtained from biomaRt", "topics": [ "TSS.mouse.GRCm38" ] }, { "page": "TSS.mouse.NCBIM37", "title": "TSS annotation data for mouse (NCBIM37) obtained from biomaRt", "topics": [ "TSS.mouse.NCBIM37" ] }, { "page": "TSS.rat.RGSC3.4", "title": "TSS annotation data for rat (RGSC3.4) obtained from biomaRt", "topics": [ "TSS.rat.RGSC3.4" ] }, { "page": "TSS.rat.Rnor_5.0", "title": "TSS annotation data for Rattus norvegicus (Rnor_5.0) obtained from biomaRt", "topics": [ "TSS.rat.Rnor_5.0" ] }, { "page": "TSS.zebrafish.Zv8", "title": "TSS annotation data for zebrafish (Zv8) obtained from biomaRt", "topics": [ "TSS.zebrafish.Zv8" ] }, { "page": "TSS.zebrafish.Zv9", "title": "TSS annotation for Danio rerio (Zv9) obtained from biomaRt", "topics": [ "TSS.zebrafish.Zv9" ] }, { "page": "TxDb2GR", "title": "TxDb object to GRanges", "topics": [ "TxDb2GR" ] }, { "page": "wgEncodeTfbsV3", "title": "transcription factor binding site clusters (V3) from ENCODE", "topics": [ "wgEncodeTfbsV3" ] }, { "page": "write2FASTA", "title": "Write sequences to a file in fasta format", "topics": [ "write2FASTA" ] }, { "page": "xget", "title": "Return the value from a Bimap objects", "topics": [ "xget" ] } ], "_readme": "https://github.com/bioc/ChIPpeakAnno/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "askpass", "BH", "Biobase", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "dplyr", "ensembldb", "farver", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "graph", "gtable", "hms", "httr", "httr2", "InteractionSet", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "multtest", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "ProtGenerics", "purrr", "pwalign", "R6", "rappdirs", "RBGL", "RColorBrewer", "Rcpp", "RcppThread", "RCurl", "regioneR", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "UCSC.utils", "universalmotif", "utf8", "vctrs", "VennDiagram", "viridisLite", "withr", "XML", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "ChIPpeakAnno.Rmd", "filename": "ChIPpeakAnno.html", "title": "ChIPpeakAnno: annotate, visualize, and compare peak data", "author": "Jianhong Ou, Kai Hu, Haibo Liu, Junhui Li, Jun Yu, Lihua Julie Zhu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Quick demo", "Convert peaks to GRanges", "Prepare annotations", "Annotate peaks", "Add gene symbols", "Convert peaks to GRanges", "Handle replicates", "Obtain final peak set from replicates", "Assess the concordance of peak replicates", "Find overlapping peaks", "Visualize the overlaps using Venn diagram", "Use other tools to plot Venn diagram", "Visualize the distribution of relative positions for overlapping peaks", "Prepare annotation file", "Commonly used annotations", "Bioconductor supported TxDb and EnsDb", "Obtain EnsDb and TxDb from AnnotationHub", "Build custom EnsDb and TxDb", "Use biomaRt", "Convert annotations into GRanges", "Use toGRanges function", "Use accessor functions", "Use getAnnotation function", "Visualize peak distributions", "Plot peak distributions relative to genomic features", "Plot peak distributions over different feature levels", "Pie graph with one peak set", "Bar graph with a list of peak sets", "Plot peak overlaps for multiple features", "Annotate peaks", "Peak-centric method", "Feature-centric method", "Relative peak-to-feature location", "More customization with bindingRegion", "Example 1: find the nearest features", "Example 2: find the nearest and overlapping features", "Visualize peak-to-feature distances", "Use custom annotation data", "Add other feature IDs", "Example1: find gene symbols for a vector of entrez IDs", "Example2: add gene symbols to annotated peaks", "Enrichment analysis", "Motif analysis", "Obtain sequences surrounding the peaks", "Discover consensus sequences (motifs) in the peaks", "Scan pre-defined sequence patterns in the peaks", "Alternative tools", "Peak profile comparison", "Use hypergeometric test to determine overlap among peak sets", "Use permutation test to determine overlap among peak sets", "Use custom peak pool", "Visualize TSS enrichment signal of multiple experiments", "Heatmap", "Density plot", "Common workflow 1: single TF with replicates", "Step1: import data", "Step2: prepare annotation file", "Step3: visualize peak distribution", "Peak distribution relative to features", "Peak distribution over multiple feature levels", "Peak overlappings for multiple features", "Step4: annotate peaks", "Find peaks located in bi-directional promoters", "Find peaks located in enhancers", "Step5: perform enrichment analysis", "Step6: conduct motif analysis", "Common workflow 2: comparing binding profiles for multiple TFs", "Step2: determine if there is significant overlap among peak sets", "Step3: visualize and compare the binding patterns", "Have questions?", "Selected Q & A", "How to import peaks?", "How to properly annotate peaks from ChIP-seq data?", "Should I use annotatePeakInBatch or annoPeaks?", "How to prepare annotation data for annotatePeakInBatch?", "Can I output either the nearest or overlapping features?", "Why is the sum of peak numbers in the Venn diagram NOT equal to the sum of the peaks in the original peak lists?", "How does findOverlapsOfPeaks count the number of overlapping peaks?", "Is there a way to show the number of peaks in original peak lists?", "How to extract the original peak IDs of the overlapping peaks?", "How to select the proper number for totalTest when using makeVennDiagram?", "How to cite ChIPpeakAnno", "Session info" ], "created": "2015-10-07 21:01:48", "modified": "2026-03-16 19:46:26", "commits": 18 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