{ "_id": "6ae6fc0d9ceaa78f2009935a", "Package": "annotatr", "Title": "Annotation of Genomic Regions to Genomic Annotations", "Version": "1.39.19", "Date": "2025-06-21", "Authors@R": "c(\nperson(\"Raymond G.\", \"Cavalcante\", email = \"rcavalca@umich.edu\", role = c(\"aut\", \"cre\")),\nperson(c(\"Maureen A.\"), \"Sartor\", email = \"sartorma@med.umich.edu\", role = c(\"ths\")))", "Description": "Given a set of genomic sites/regions (e.g. ChIP-seq peaks,\nCpGs, differentially methylated CpGs or regions, SNPs, etc.) it\nis often of interest to investigate the intersecting genomic\nannotations. Such annotations include those relating to gene\nmodels (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs\n(CpG islands, CpG shores, CpG shelves), or regulatory sequences\nsuch as enhancers. The annotatr package provides an easy way to\nsummarize and visualize the intersection of genomic\nsites/regions with genomic annotations.", "VignetteBuilder": "knitr", "BugReports": "https://www.github.com/rcavalcante/annotatr/issues", "License": "GPL-3", "LazyData": "true", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "Config/testthat/edition": "3", "biocViews": "Software, Annotation, GenomeAnnotation, FunctionalGenomics,\nVisualization", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-10-02 09:19:56 UTC", "RemoteUrl": "https://github.com/bioc/annotatr", "RemoteRef": "HEAD", "RemoteSha": "4567918a24fffbc2bbf78c0cb73fc82b444bca1c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-01 08:24:25 UTC", "User": "root" }, "Author": "Raymond G. Cavalcante [aut, cre],\nMaureen A. Sartor [ths]", "Maintainer": "Raymond G. 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], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.39.19", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.38.3", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "software", "annotation", "genomeannotation", "functionalgenomics", "visualization", "genome-annotation" ], "_stars": 27, "_contributors": [ { "user": "rcavalcante", "count": 68, "uuid": 626455 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "hpages", "count": 6, "uuid": 8810451 }, { "user": "kdkorthauer", "count": 2, "uuid": 14237017 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "link-ny", "count": 1, "uuid": 4392950 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 481, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 1380, "source": 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build annotations from TxDb.* and AnnotationHub resources", "topics": [ "build_annotations" ] }, { "page": "build_ccre_annots", "title": "A helper function to build ENCODE cCRE annotations.", "topics": [ "build_ccre_annots" ] }, { "page": "build_cpg_annots", "title": "A helper function to build CpG related annotations.", "topics": [ "build_cpg_annots" ] }, { "page": "build_enhancer_annots", "title": "A helper function to build enhancer annotations for hg19 and mm10 from FANTOM5.", "topics": [ "build_enhancer_annots" ] }, { "page": "build_gene_annots", "title": "A helper function to build genic annotations.", "topics": [ "build_gene_annots" ] }, { "page": "build_hmm_annots", "title": "A helper function to build chromHMM annotations for hg19 from UCSC Genome Browser.", "topics": [ "build_hmm_annots" ] }, { "page": "build_lncrna_annots", "title": "A helper function to build lncRNA annotations.", "topics": [ "build_lncrna_annots" ] }, { "page": "build_mane_txdb", "title": "Function to build a TxDb of the MANE Select transcripts", "topics": [ "build_mane_txdb" ] }, { "page": "build_txdb_annotations", "title": "Build gene annotations from any TxDb or EnsDb", "topics": [ "build_txdb_annotations" ] }, { "page": "build_txdb_gene_annots", "title": "A helper function to build genic annotations from a TxDb or EnsDb", "topics": [ "build_txdb_gene_annots" ] }, { "page": "builtin_annotations", "title": "Function listing which annotations are available.", "topics": [ "builtin_annotations" ] }, { "page": "builtin_annotations_table", "title": "Table of builtin annotations by genome", "topics": [ "builtin_annotations_table" ] }, { "page": "builtin_genomes", "title": "Function returning supported TxDb.* genomes", "topics": [ "builtin_genomes" ] }, { "page": "cached-annotations", "title": "Cached annotations", "topics": [ "cached-annotations" ] }, { "page": "check_annotations", "title": "Function to check for valid annotations", "topics": [ "check_annotations" ] }, { "page": "check_regions_genome", "title": "Function to check regions and annotations are from the same genome", "topics": [ "check_regions_genome" ] }, { "page": "clear_cached_annotations", "title": "Clear cached annotations and downloads", "topics": [ "clear_cached_annotations" ] }, { "page": "coannotation_pairs", "title": "Function to find the pairs of annotation types on each region", "topics": [ "coannotation_pairs" ] }, { "page": "download_annotation_file", "title": "Function to download a file, with retries, into the cache", "topics": [ "download_annotation_file" ] }, { "page": "expand_annotations", "title": "Function to expand annotation shortcuts", "topics": [ "expand_annotations" ] }, { "page": "get_annotation_rname", "title": "Function to get the cache resource name of a built annotation", "topics": [ "get_annotation_rname" ] }, { "page": "get_bfc", "title": "Function to get the BiocFileCache for the cache", "topics": [ "get_bfc" ] }, { "page": "get_cache_dir", "title": "Function to get the directory of the cache", "topics": [ "get_cache_dir" ] }, { "page": "get_cache_rids", "title": "Function to get the resource IDs of cache entries", "topics": [ "get_cache_rids" ] }, { "page": "get_cellline_from_code", "title": "Function to return cell line from chromatin annotation code", "topics": [ "get_cellline_from_code" ] }, { "page": "get_cellline_from_shortcut", "title": "Function to return cell line from chromatin annotation shortcut", "topics": [ "get_cellline_from_shortcut" ] }, { "page": "get_chrom_aliases", "title": "Function to map any chromosome alias of a genome to its UCSC-style name", "topics": [ "get_chrom_aliases" ] }, { "page": "get_genark_seqinfo", "title": "Function to get the Seqinfo of a GenArk genome with UCSC-style names", "topics": [ "get_genark_seqinfo" ] }, { "page": "get_genark_url", "title": "Function to get the URL of a file in the UCSC GenArk hub for a genome", "topics": [ "get_genark_url" ] }, { "page": "get_gene_table", "title": "Function to map gene IDs to gene symbols, Entrez IDs, and Ensembl IDs", "topics": [ "get_gene_table" ] }, { "page": "get_mane_summary", "title": "Function to get the MANE Select summary", "topics": [ "get_mane_summary" ] }, { "page": "get_orgdb_name", "title": "Function to get correct org.* package name based on genome", "topics": [ "get_orgdb_name" ] }, { "page": "get_txdb_name", "title": "Function to get correct TxDb.* package name based on genome", "topics": [ "get_txdb_name" ] }, { "page": "list_cached_annotations", "title": "List cached annotations and downloads", "topics": [ "list_cached_annotations" ] }, { "page": "load_cached_annotation", "title": "Function to load a built annotation from the cache", "topics": [ "load_cached_annotation" ] }, { "page": "plot_annotation", "title": "Plot the number of regions per annotation", "topics": [ "plot_annotation" ] }, { "page": "plot_categorical", "title": "Plot a categorical data variable over another", "topics": [ "plot_categorical" ] }, { "page": "plot_coannotations", "title": "Plot pair-wise annotations across regions", "topics": [ "plot_coannotations" ] }, { "page": "plot_numerical", "title": "Plot numerical data over regions or regions summarized over annotations", "topics": [ "plot_numerical" ] }, { "page": "plot_numerical_coannotations", "title": "Plot numerical data occurring in pairs of annotations", "topics": [ "plot_numerical_coannotations" ] }, { "page": "randomize_regions", "title": "Randomize Regions", "topics": [ "randomize_regions" ] }, { "page": "read_annotations", "title": "Read custom annotations", "topics": [ "read_annotations" ] }, { "page": "read_ccre_bed", "title": "Function to read an ENCODE cCRE registry BED file", "topics": [ "read_ccre_bed" ] }, { "page": "read_regions", "title": "Read genomic regions in BEDX+Y format", "topics": [ "read_regions" ] }, { "page": "reformat_hmm_codes", "title": "Function to recode classes from chromHMM type column", "topics": [ "reformat_hmm_codes" ] }, { "page": 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