To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

annotatr

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see annotatr.

Annotation of Genomic Regions to Genomic Annotations

Bioconductor version: 3.4

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

HTML R Script Vignette Title
PDF Reference Manual
Text NEWS

Details

biocViews Annotation, FunctionalGenomics, GenomeAnnotation, Software, Visualization
Version 1.0.3
In Bioconductor since BioC 3.4 (R-3.3) (0.5 years)
License GPL-3
Depends R (>= 3.3.0)
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.

Package Source annotatr_1.0.3.tar.gz
Windows Binary annotatr_1.0.3.zip
Mac OS X 10.9 (Mavericks) annotatr_1.0.3.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/annotatr/tree/release-3.4
Package Short Url http://bioconductor.org/packages/annotatr/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

AltStyle によって変換されたページ (->オリジナル) /