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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("OrganismDbi")
In most cases, you don't need to download the package archive at all.
OrganismDbi
Software to enable the smooth interfacing of different database packages.
Bioconductor version: 3.0
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, Herve Pages, Martin Morgan, Valerie Obenchain
Maintainer: Biocore Data Team <maintainer at bioconductor.org>
Citation (from within R,
enter citation("OrganismDbi")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("OrganismDbi")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("OrganismDbi")
| R Script | OrganismDbi: A meta framework for Annotation Packages | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, Infrastructure, Software |
| Version | 1.8.1 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | Artistic-2.0 |
| Depends | R (>= 2.14.0), methods, AnnotationDbi(>= 1.16.10), GenomicFeatures(>= 1.17.13) |
| Imports | BiocGenerics, graph, RBGL, AnnotationDbi, stats |
| LinkingTo | |
| Suggests | Homo.sapiens, Rattus.norvegicus, RUnit |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | Homo.sapiens, Mus.musculus, Rattus.norvegicus |
| Imports Me | epivizr, ggbio |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | OrganismDbi_1.8.1.tar.gz |
| Windows Binary | OrganismDbi_1.8.1.zip |
| Mac OS X 10.6 (Snow Leopard) | OrganismDbi_1.8.1.tgz |
| Mac OS X 10.9 (Mavericks) | OrganismDbi_1.8.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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