OrganismDbi

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

• Version: 1.54.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: BiocGenerics, AnnotationDbi, Seqinfo, GenomicFeatures
• Imports: DBI, BiocManager, Biobase, graph, RBGL, S4Vectors, IRanges, GenomicRanges
• System requirements: URL
• Install: BiocManager::install("OrganismDbi")

When to Use

• Unified Annotation Queries: Querying multiple annotation resources (e.g., TxDb and OrgDb) simultaneously through a single unified interface using select.
• Custom Meta-Package Building: Building custom OrganismDbi meta-packages (like Homo.sapiens) that link genome-centric and gene-centric databases using makeOrganismPackage.
• Feature Extraction: Extracting genomic features (transcripts, exons, cds) mapped directly to gene symbols or other identifiers using transcripts, exons, or cds.
• Grouped Feature Extraction: Grouping genomic features by a specific identifier (e.g., by gene) using transcriptsBy, exonsBy, or cdsBy.

When NOT to Use

• Non-Model Organisms: When working with non-model organisms that do not have pre-built OrgDb or TxDb packages available to link together.
• Cyclic Graph Relationships: When the relationships between your annotation packages present more than one pathway between any two nodes/objects (the package cannot handle cycles in the graph).

Data Requirements

• Annotation Packages: Installed Bioconductor annotation packages (e.g., org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, GO.db).
• Graph Data: A list of short two-element character vectors representing foreign key relationships (e.g., graphData) when building custom packages.