annotatr

Annotation of Genomic Regions to Genomic Annotations


Bioconductor version: Release (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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("annotatr")

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

Documentation

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

browseVignettes("annotatr")
annotatr HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, FunctionalGenomics, GenomeAnnotation, Software, Visualization
Version 1.30.0
In Bioconductor since BioC 3.4 (R-3.3) (8 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
URL
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
Enhances
Depends On Me
Imports Me SOMNiBUS, dmrseq, scmeth, ExpHunterSuite
Suggests Me borealis, methodical, ramr
Links To Me
Build Report Build Report

Package Archives

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

Source Package annotatr_1.30.0.tar.gz
Windows Binary (x86_64) annotatr_1.30.0.zip
macOS Binary (x86_64) annotatr_1.30.0.tgz
macOS Binary (arm64) annotatr_1.30.0.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/
Package Downloads Report Download Stats