NEWS

txdbmaker 1.8.0

Add Taxonomy ID to TxDb object returned by makeTxDbFromEnsembl(). Like for other makeTxDbFrom*() functions, the new 'taxonomyId' argument of makeTxDbFromEnsembl() is set to NA by default. So if the user doesn't supply a Taxonomy ID via the argument, GenomeInfoDb:::lookup_tax_id_by_organism() is used to retrieve the taxonomy ID for the supplied 'organism'. Otherwise GenomeInfoDb:::check_tax_id() is used to check the user-supplied taxonomy ID. Contributed by I-Hsuan Lin.

Deprecate functions supportedUCSCFeatureDbTracks() and supportedUCSCFeatureDbTables(). Use list_UCSC_tracks() from package UCSC.utils instead.
Deprecate the 'track', 'url', and 'goldenPath.url' arguments of functions makeFeatureDbFromUCSC() and UCSCFeatureDbTableSchema().
Utility function supportedMiRBaseBuildValues(), argument 'miRBaseBuild', and argument 'port' are now gone after being defunct in BioC 3.22. Note that 'miRBaseBuild' and 'port' were arguments of several functions in the txdbmaker package.

Add Seqinfo to Depends and move GenomeInfoDb to Imports.
Drop mirbase.db from Suggests (package got removed from BioC 3.22 after being deprecated in BioC 3.21). As a consequence, utility function supportedMiRBaseBuildValues() and argument 'miRBaseBuild' are now defunct (the latter is an argument of various functions in the package).

Utility function supportedMiRBaseBuildValues() and argument 'miRBaseBuild' are defunct (the latter is an argument of various functions in the package).

Add genome version to TxDb returned by makeTxDbFromEnsembl(). Author: Robert Castelo

Adjust makeTxDbFromBiomart() examples to reflect breaking change in Ensembl 113. See commit a5a885d for the details.

Small fix to internal helper .Ensembl_getMySQLCoreDir(). See commit aa586a6 for the details.

The txdbmaker package is a spin-off from the GenomicFeatures package. It includes the following functions, all of them originally from the GenomicFeatures package: - browseUCSCtrack - getChromInfoFromBiomart - makeFDbPackageFromUCSC - makeFeatureDbFromUCSC - makePackageName - makeTxDb - makeTxDbFromBiomart - makeTxDbFromEnsembl - makeTxDbFromGFF - makeTxDbFromGRanges - makeTxDbFromUCSC - makeTxDbPackage - makeTxDbPackageFromBiomart - makeTxDbPackageFromUCSC - supportedMiRBaseBuildValues - supportedUCSCFeatureDbTables - supportedUCSCFeatureDbTracks - supportedUCSCtables - UCSCFeatureDbTableSchema