annotatr
This is the development version of annotatr; for the stable release version, see annotatr.
Annotation of Genomic Regions to Genomic Annotations
Bioconductor version: Development (3.24)
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")):Raymond G. Cavalcante. annotatr: Annotation of Genomic Regions to Genomic Annotations. doi:10.18129/B9.bioc.annotatr, R package version 1.39.19, https://bioconductor.org/packages/annotatr.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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")| annotatr | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, FunctionalGenomics, GenomeAnnotation, Software, Visualization |
| Version | 1.39.19 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 years) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | AnnotationDbi, AnnotationHub, BiocFileCache, dplyr, GenomicFeatures (>= 1.61.4), GenomicRanges (>= 1.61.1), Seqinfo, ggplot2 (>= 3.5.0), IRanges, methods, readr, regioneR, reshape2, rlang, rtracklayer (>= 1.69.1), S4Vectors (>= 0.23.10), stats, utils |
| System Requirements | |
| URL | |
| Bug Reports | https://www.github.com/rcavalcante/annotatr/issues |
See More
| Suggests | GenomeInfoDb, BiocStyle, curl, devtools, ensembldb, knitr, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat (>= 3.2.0), txdbmaker, withr, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Drerio.UCSC.danRer11.refGene, 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.Mmusculus.UCSC.mm39.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | dmrseq, epiRomics, ExpHunterSuite, scmeth, SOMNiBUS |
| Suggests Me | borealis, ramr |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | annotatr_1.39.19.tar.gz |
| Windows Binary (x86_64) | annotatr_1.39.19.zip |
| macOS Binary (big-sur-x86_64) | annotatr_1.39.19.tgz |
| macOS Binary (sonoma-arm64) | annotatr_1.39.19.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/annotatr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/annotatr |
| Package Short Url | https://bioconductor.org/packages/annotatr/ |
| Package Downloads Report | Download Stats |