Bioconductor - annotatr

Bioconductor - annotatr
Bioconductor 3.22
Software Packages
annotatr
annotatr
This is the
released
version of annotatr; for the devel version, see
annotatr
Annotation of Genomic Regions to Genomic Annotations
DOI:
10.18129/B9.bioc.annotatr
Bioconductor version:
Release (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
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")

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
PDF
NEWS
Text
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
Annotation
FunctionalGenomics
GenomeAnnotation
Software
Visualization
Version
1.36.0
In Bioconductor since
BioC 3.4 (R-3.3) (9.5 years)
License
GPL-3
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
System Requirements
URL
Bug Reports
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.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
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.
Source Package
annotatr_1.36.0.tar.gz
Windows Binary (x86_64)
annotatr_1.36.0.zip
macOS Binary (x86_64)
annotatr_1.36.0.tgz
macOS Binary (arm64)
annotatr_1.36.0.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
Package Short Url
Package Downloads Report
Download Stats