annotatr

Annotation of Genomic Regions to Genomic Annotations

Bioconductor version: Release (3.17)

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 "4.3") 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	1.26.0
In Bioconductor since	BioC 3.4 (R-3.3) (7 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
Linking To
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
System Requirements
Enhances
URL
Bug Reports	https://www.github.com/rcavalcante/annotatr/issues

Depends On Me
Imports Me	dmrseq, scmeth
Suggests Me	borealis, ramr
Links To Me
Build Report

Package Archives

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

Source Package	annotatr_1.26.0.tar.gz
Windows Binary	annotatr_1.26.0.zip
macOS Binary (x86_64)	annotatr_1.26.0.tgz
macOS Binary (arm64)	annotatr_1.26.0.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