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>

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

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

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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/
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Old Source Packages for BioC 3.6 Source Archive

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