annotatr
Annotation of Genomic Regions to Genomic Annotations
Bioconductor version: 3.23 · Package version: 1.38.3
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("annotatr")Details
| Maintainer | Raymond G. Cavalcante <rcavalca@umich.edu> |
| Author | Raymond G. Cavalcante [aut, cre], Maureen A. Sartor [ths] |
| License | GPL-3 |
| Bug Reports | https://www.github.com/rcavalcante/annotatr/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, FunctionalGenomics, GenomeAnnotation, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/annotatr/ |
Citation
From within R, enter citation("annotatr"):
Raymond G. Cavalcante. annotatr: Annotation of Genomic Regions to Genomic Annotations. doi:10.18129/B9.bioc.annotatr, R package version 1.38.3, https://bioconductor.org/packages/annotatr.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | annotatr_1.38.3.tar.gz |
| Windows binary (x86_64) | annotatr_1.38.0.zip |
| macOS binary (arm64) | annotatr_1.38.0.tgz |
| macOS binary (x86_64) | annotatr_1.38.0.tgz |
Dependencies
Depends: R (>= 3.5.0)
Imports: AnnotationDbi, AnnotationHub, 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
Suggests: GenomeInfoDb, 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.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