sitadela
sitadela is a Bioconductor package for the construction and maintenance of versioned genomic interval annotations for a variety of genomes as well as custom organisms. Features include:
- Simple tab-delimited genomic interval annotations for several transcription unit types with additional characteristics (gene GC content, biotypes).
- A centralized annotation building and retrieval system, supporting several organisms, versions and annotation resources as well as custom user annotations coming in GTF/GFF format.
- Versioning of the annotation builds to improve reproducibility and tracking.
- A unified interface to several genomic interval annotation sources which automates database build but also fetches annotations on-the-fly if not already present in the build.
- Centralized gene and transcript versioning where available (e.g. NCBI), especially useful for genomics precision medicine applications and the respective diagnostic processes.
- Additional portability from Bioconductor to other applications through the simple database schema adopted.
- Additional attributes such as corrected feature lengths (i.e. corrected gene lengths based on sum of lengths of coding regions, to be used e.g. for RNA abundance).
sitadela powers the annotation system behind metaseqR2 and recoup.
Availability: