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Bioconductor / txdbmaker

A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files)
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Updating miRBase annotations for `makeTxDbFromGFF` to support GRCh38 #4

Open mjsteinbaugh opened 3 years ago

mjsteinbaugh commented 3 years ago

makeTxDbFromGFF supports the miRBaseBuild argument:

Specify the string for the appropriate build Information from mirbase.db to use for microRNAs. This can be learned by calling supportedMiRBaseBuildValues. By default, this value will be set to NA, which will inactivate the microRNAs accessor.

Calling txdbmaker::supportedMiRBaseBuildValues() returns a data.frame of supported genome assemblies. Unforunately GRCh38 for Homo sapiens isn't included because the annotations are out of date. These are defined in the mirbase.db package, which hasn't been updated since 2013. For reference, miRBase does support GRCh38 annotations.

I'm open to helping add access to GRCh38 miRBase annotations in txdbmaker. What's the best way to approach this? By working on an update to mirbase.db?

mjsteinbaugh commented 3 years ago

miRBaseVersions.db appears to be potentially relevant.