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Bioconductor - annotatr (development version)

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 (3.22)

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 (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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")

Details biocViews Annotation, FunctionalGenomics, GenomeAnnotation, Software, Visualization Version 1.35.1 In Bioconductor since BioC 3.4 (R-3.3) (8.5 years) License GPL-3 Depends R (>= 3.5.0) Imports AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures(>= 1.61.4), GenomicRanges(>= 1.61.1), Seqinfo, ggplot2, IRanges, methods, readr, regioneR, reshape2, 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, 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, methodical, scmeth, SOMNiBUS, ExpHunterSuite Suggests Me borealis, ramr Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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