annotatr
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see annotatr.
Annotation of Genomic Regions to Genomic Annotations
Bioconductor version: 3.10
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("annotatr")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("annotatr")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("annotatr")| Vignette Title | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, FunctionalGenomics, GenomeAnnotation, Software, Visualization |
| Version | 1.12.1 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.4.0) |
| Imports | AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures, GenomicRanges, GenomeInfoDb(>= 1.10.3), ggplot2, IRanges, methods, readr, regioneR, reshape2, rtracklayer, S4Vectors(>= 0.23.10), stats, utils |
| System Requirements | |
| URL | |
| Bug Reports | https://www.github.com/rcavalcante/annotatr/issues |
See More
| Suggests | BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | dmrseq, scmeth |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | annotatr_1.12.1.tar.gz |
| Windows Binary | annotatr_1.12.1.zip |
| Mac OS X 10.11 (El Capitan) | annotatr_1.12.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/annotatr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/annotatr |
| Bioc Package Browser | https://code.bioconductor.org/browse/annotatr/ |
| Package Short Url | https://bioconductor.org/packages/annotatr/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |