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")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("annotatr")
HTML | R Script | Vignette Title |
Reference Manual | ||
Text | NEWS |
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 |
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 |
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