Organism.dplyr

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see Organism.dplyr.

All versions

3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5

dplyr-based Access to Bioconductor Annotation Resources

Bioconductor version: Release (3.23)

This package provides an alternative interface to Bioconductor 'annotation' resources, in particular the gene identifier mapping functionality of the 'org' packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the 'TxDb' packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

Author: Martin Morgan [aut, cre], Daniel van Twisk [ctb], Yubo Cheng [aut]

Maintainer: Martin Morgan <martin.morgan at roswellpark.org>

Citation (from within R, enter citation("Organism.dplyr")):

Martin Morgan, Yubo Cheng. Organism.dplyr: dplyr-based Access to Bioconductor Annotation Resources. doi:10.18129/B9.bioc.Organism.dplyr, R package version 1.40.0, https://bioconductor.org/packages/Organism.dplyr.

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")

BiocManager::install("Organism.dplyr")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

No vignettes available
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, GenomeAnnotation, Sequencing, Software
Version	1.40.0
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 years)
License	Artistic-2.0
Depends	R (>= 4.1.0), dplyr (>= 0.7.0), AnnotationFilter (>= 1.1.3)
Imports	RSQLite, S4Vectors, Seqinfo, IRanges, GenomicRanges (>= 1.61.1), GenomicFeatures (>= 1.61.4), AnnotationDbi, rlang, methods, tools, utils, BiocFileCache, DBI, dbplyr, tibble
System Requirements
URL
Bug Reports	https://github.com/Bioconductor/Organism.dplyr/issues

Suggests	GenomeInfoDb, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, magick, BiocStyle, ggplot2
Linking To
Enhances
Depends On Me
Imports Me	linkSet, Ularcirc
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/Organism.dplyr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Organism.dplyr
Package Short Url	https://bioconductor.org/packages/Organism.dplyr/
Package Downloads Report	Download Stats