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.
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("Organism.dplyr")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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
| Reference Manual |
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 |
See More
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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 |