NEWS
txdbmaker 1.8.0
NEW FEATURES
- 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.
DEPRECATED AND DEFUNCT
- 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.
txdbmaker 1.6.0
SIGNIFICANT USER-VISIBLE CHANGES
- 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).
DEPRECATED AND DEFUNCT
- Utility function supportedMiRBaseBuildValues() and argument
'miRBaseBuild' are defunct (the latter is an argument of various
functions in the package).
txdbmaker 1.4.0
SIGNIFICANT USER-VISIBLE CHANGES
- Add genome version to TxDb returned by makeTxDbFromEnsembl().
Author: Robert Castelo
BUG FIXES
- Fix bug in supportedUCSCtables(). See commit 05d278f for the details.
txdbmaker 1.2.0
SIGNIFICANT USER-VISIBLE CHANGES
- Adjust makeTxDbFromBiomart() examples to reflect breaking change
in Ensembl 113. See commit a5a885d for the details.
BUG FIXES
- Small fix to internal helper .Ensembl_getMySQLCoreDir(). See commit
aa586a6 for the details.
txdbmaker 1.0.0
- 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