OrganismDbi
Software to enable the smooth interfacing of different database packages
Bioconductor version: Release (3.19)
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")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.46.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (12 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.14.0), BiocGenerics(>= 0.15.10), AnnotationDbi(>= 1.33.15), GenomicFeatures(>= 1.39.4) |
| Imports | methods, utils, stats, DBI, BiocManager, Biobase, graph, RBGL, S4Vectors, IRanges, GenomicRanges(>= 1.31.13), txdbmaker |
| System Requirements | |
| URL |
See More
| Suggests | Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, 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_1.46.0.tar.gz |
| Windows Binary (x86_64) | OrganismDbi_1.46.0.zip |
| macOS Binary (x86_64) | OrganismDbi_1.46.0.tgz |
| macOS Binary (arm64) | OrganismDbi_1.46.0.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 |