CHANGES IN VERSION 1.8 ----------------------- NEW FEATURES o Added asBED and asGFF methods to convert a TranscriptDb to a GRanges that describes transcript structures according to either the BED or GFF format. This enables passing a TranscriptDb object to rtracklayer::export directly, when targeting GFF/BED. CHANGES IN VERSION 1.6 ----------------------- NEW FEATURES o TranscriptDbs are now available as standard packages. Functions that were made available before the last release allow users to create these packages. o TranscriptDb objects now can be used with select o select method for TranscriptDb objects to extract data.frames of available annotations. Users can specify keys, along with the keytype, and the columns of data that they want extracted from the annotation package. o keys now will operate on TranscriptDB objects to expose ID types as potential keys o keytypes will show which kinds of IDs can be used as a key by select o cols will display the kinds of data that can be extracted by select o isActiveSeq has been added to allow entire chromosomes to be toggled active/inactive by the user. By default, everything is exposed, but if you wish you can now easily hide everything that you don't want to see. Subsequence to this, all your accessors will behave as if only the "active" things are present in the database. SIGNIFICANT USER-VISIBLE CHANGES o saveDb and loadDb are here and will be replacing saveFeatures and loadFeatures. The reason for the name change is that they dispatch on (and should work with a wider range of object types than just trancriptDb objects (and their associated databases). BUG FIXES o ORDER BY clause has been added to SQL statements to enforce more consistent ordering of returned rows. o bug fixes to enable DB construction to still work even after changes in schemas etc at UCSC, and ensembl sources. o bug fixes to makeFeatureDbFromUCSC allow it to work more reliably (it was being a little too optimistic about what UCSC would actually supply data for)