Organism.dplyr

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see Organism.dplyr.

dplyr-based Access to Bioconductor Annotation Resources

Bioconductor version: 3.13

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")):

Installation

To install this package, start R (version "4.1") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Organism.dplyr")

Organism.dplyr HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, GenomeAnnotation, Sequencing, Software

Version 1.20.0

In Bioconductor since BioC 3.5 (R-3.4) (7 years)

License Artistic-2.0

Depends R (>= 3.4), dplyr (>= 0.7.0), AnnotationFilter(>= 1.1.3)

Imports RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges, GenomicFeatures, AnnotationDbi, rlang, methods, tools, utils, BiocFileCache, DBI, dbplyr, tibble

System Requirements

URL

Suggests org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, BiocStyle, ggplot2

Linking To

Enhances

Depends On Me annotation

Imports Me Ularcirc

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package Organism.dplyr_1.20.0.tar.gz

Windows Binary Organism.dplyr_1.20.0.zip

macOS 10.13 (High Sierra) Organism.dplyr_1.20.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/Organism.dplyr

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Organism.dplyr

Bioc Package Browser https://code.bioconductor.org/browse/Organism.dplyr/

Package Short Url https://bioconductor.org/packages/Organism.dplyr/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.13 Source Archive