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Tool Description Pros Cons | ||
**[org.Xx.eg.db](https://bioconductor.org/packages/release/bioc/vignettes/AnnotationDbi/inst/doc/IntroToAnnotationPackages.pdf)** Query gene feature information for the organism of interest gene ID conversion, biotype and coordinate information only latest genome build available | ||
**[EnsDb.Xx.vxx](http://bioconductor.org/packages/devel/bioc/vignettes/ensembldb/inst/doc/ensembldb.html)** Transcript and gene-level information directly fetched from Ensembl API (similar to TxDb, but with filtering ability and versioned by Ensembl release) easy functions to extract features, direct filtering Not the most up-to-date annotations, more difficult to use than some packages | ||
**[TxDb.Xx.UCSC.hgxx.knownGene](https://bioconductor.org/packages/release/bioc/vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf)** UCSC database for transcript and gene-level information or can create own *TxDb* from an SQLite database file using the *GenomicFeatures* package feature information, easy functions to extract features only available current and recent genome builds - can create your own, less up-to-date with annotations than Ensembl | ||
**[annotables](https://github.com/stephenturner/annotables)** Gene-level feature information immediately available for the human and model organisms super quick and easy gene ID conversion, biotype and coordinate information static resource, not updated regularly | ||
**[biomaRt](https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html)** An R package version of the Ensembl [BioMart online tool](http://www.ensembl.org/biomart/martview/70dbbbe3f1c5389418b5ea1e02d89af3) all Ensembl database information available, all organisms on Ensembl, wealth of information |
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