annotatr

DOI: 10.18129/B9.bioc.annotatr    

Annotation of Genomic Regions to Genomic Annotations

Bioconductor version: Release (3.6)

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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("annotatr")

Documentation

HTML	R Script	Vignette Title
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, FunctionalGenomics, GenomeAnnotation, Software, Visualization
Version	1.4.1
In Bioconductor since	BioC 3.4 (R-3.3) (1.5 years)
License	GPL-3
Depends	R (>= 3.4.0)
Imports	AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures, GenomicRanges, GenomeInfoDb(>= 1.10.3), ggplot2, IRanges, methods, org.Dm.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, readr, regioneR, reshape2, rtracklayer, S4Vectors, stats, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, 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, utils
LinkingTo
Suggests	BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat
SystemRequirements
Enhances
URL
BugReports	https://www.github.com/rcavalcante/annotatr/issues
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	annotatr_1.4.1.tar.gz
Windows Binary	annotatr_1.4.1.zip
Mac OS X 10.11 (El Capitan)	annotatr_1.4.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/annotatr
Package Short Url	http://bioconductor.org/packages/annotatr/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive