OrganismDbi
This is the development version of OrganismDbi; for the stable release version, see OrganismDbi.
Software to enable the smooth interfacing of different database packages
Bioconductor version: Development (3.24)
The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.
Author: Marc Carlson [aut], Martin Morgan [aut], Valerie Obenchain [aut], Aliyu Atiku Mustapha [ctb] (Converted 'OrganismDbi' vignette from Sweave to RMarkdown / HTML.), Bioconductor Package Maintainer [cre]
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
citation("OrganismDbi")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("OrganismDbi")
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("OrganismDbi")| OrganismDbi: A meta framework for Annotation Packages | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Infrastructure, Software |
| Version | 1.55.1 |
| In Bioconductor since | BioC 2.11 (R-2.15) (14 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.14.0), BiocGenerics(>= 0.15.10), AnnotationDbi(>= 1.33.15), Seqinfo, GenomicFeatures(>= 1.61.4) |
| Imports | methods, utils, stats, DBI, BiocManager, Biobase, graph, RBGL, S4Vectors, IRanges, GenomicRanges(>= 1.61.1) |
| System Requirements | |
| URL |
See More
| Suggests | txdbmaker, GenomeInfoDbData, Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | Homo.sapiens, Mus.musculus, Rattus.norvegicus |
| Imports Me | AnnotationHubData, epivizrData, ggbio, uncoverappLib |
| Suggests Me | ChIPpeakAnno, epivizrStandalone |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | OrganismDbi_1.55.1.tar.gz |
| Windows Binary (x86_64) | OrganismDbi_1.55.1.zip |
| macOS Binary (big-sur-x86_64) | OrganismDbi_1.55.1.tgz |
| macOS Binary (sonoma-arm64) | OrganismDbi_1.55.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/OrganismDbi |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/OrganismDbi |
| Bioc Package Browser | https://code.bioconductor.org/browse/OrganismDbi/ |
| Package Short Url | https://bioconductor.org/packages/OrganismDbi/ |
| Package Downloads Report | Download Stats |