Package: annotatr
Title: Annotation of Genomic Regions to Genomic Annotations
Version: 1.39.0
Date: 2025-06-21
Authors@R: c(
    person("Raymond G.", "Cavalcante", email = "rcavalca@umich.edu", role = c("aut", "cre")),
    person(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,
        CpGs, differentially methylated CpGs or regions, SNPs, etc.) it
        is often of interest to investigate the intersecting genomic
        annotations. Such annotations include those relating to gene
        models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs
        (CpG islands, CpG shores, CpG shelves), or regulatory sequences
        such as enhancers. The annotatr package provides an easy way to
        summarize and visualize the intersection of genomic
        sites/regions with genomic annotations.
Depends: R (>= 3.5.0)
Imports: AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures (>=
        1.61.4), GenomicRanges (>= 1.61.1), Seqinfo, ggplot2 (>=
        3.5.0), IRanges, methods, readr, regioneR, reshape2, rlang,
        rtracklayer (>= 1.69.1), S4Vectors (>= 0.23.10), stats, utils
Suggests: GenomeInfoDb, BiocStyle, devtools, knitr, org.Dm.eg.db,
        org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db,
        rmarkdown, roxygen2, testthat,
        TxDb.Dmelanogaster.UCSC.dm3.ensGene,
        TxDb.Dmelanogaster.UCSC.dm6.ensGene,
        TxDb.Drerio.UCSC.danRer10.refGene,
        TxDb.Drerio.UCSC.danRer11.refGene,
        TxDb.Ggallus.UCSC.galGal5.refGene,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene,
        TxDb.Mmusculus.UCSC.mm9.knownGene,
        TxDb.Mmusculus.UCSC.mm10.knownGene,
        TxDb.Mmusculus.UCSC.mm39.knownGene,
        TxDb.Rnorvegicus.UCSC.rn4.ensGene,
        TxDb.Rnorvegicus.UCSC.rn5.refGene,
        TxDb.Rnorvegicus.UCSC.rn6.refGene,
        TxDb.Rnorvegicus.UCSC.rn7.refGene
VignetteBuilder: knitr
BugReports: https://www.github.com/rcavalcante/annotatr/issues
License: GPL-3
LazyData: true
RoxygenNote: 7.3.3
Encoding: UTF-8
biocViews: Software, Annotation, GenomeAnnotation, FunctionalGenomics,
        Visualization
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:44:33 UTC
RemoteUrl: https://github.com/bioc/annotatr
RemoteRef: HEAD
RemoteSha: 1cae07bfcd16a37f53c168cc8e01a6b0b3248673
NeedsCompilation: no
Packaged: 2026-05-30 09:20:59 UTC; root
Author: Raymond G. Cavalcante [aut, cre],
  Maureen A. Sartor [ths]
Maintainer: Raymond G. Cavalcante <rcavalca@umich.edu>
Built: R 4.6.0; ; 2026-05-30 09:35:54 UTC; windows
