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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 |
| 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 |
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