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This is the development version of annotatr; for the stable release version, see annotatr.

Annotation of Genomic Regions to Genomic Annotations

Bioconductor version: Development (3.19)

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.

Author: Raymond G. Cavalcante [aut, cre], Maureen A. Sartor [ths]

Maintainer: Raymond G. Cavalcante <rcavalca at umich.edu>

Citation (from within R, enter citation("annotatr")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

annotatr HTML R Script
Reference Manual PDF


biocViews Annotation, FunctionalGenomics, GenomeAnnotation, Software, Visualization
Version 1.29.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL-3
Depends R (>= 3.5.0)
Imports AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures, GenomicRanges, GenomeInfoDb(>= 1.10.3), ggplot2, IRanges, methods, readr, regioneR, reshape2, rtracklayer, S4Vectors(>= 0.23.10), stats, utils
System Requirements
Bug Reports https://www.github.com/rcavalcante/annotatr/issues
See More
Suggests 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.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.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene
Linking To
Depends On Me
Imports Me dmrseq, ExpHunterSuite, scmeth, SOMNiBUS
Suggests Me borealis, methodical, ramr
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package annotatr_1.29.0.tar.gz
Windows Binary annotatr_1.29.0.zip
macOS Binary (x86_64) annotatr_1.29.0.tgz
macOS Binary (arm64) annotatr_1.29.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/annotatr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/annotatr
Bioc Package Browser https://code.bioconductor.org/browse/annotatr/
Package Short Url https://bioconductor.org/packages/annotatr/
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