[Bioc-devel] New 2.1.4 Annotation packages in R-devel branch
mcarlson at fhcrc.org
Sat Apr 12 00:33:20 CEST 2008
This is an announcement for those of you who care about annotation the
I recently released a large number of new annotation packages to the
development branch. These packages can be pretty easily spotted by
their 2.1.4 version numbers. They are based on the very latest data
sources that were available on April 2nd 2008. Please try out packages
that are of interest to you and please be sure to let me know if you
find any problems.
Some things to note: this will be the last time we make non sqlite based
annotation packages for the following organisms:
The packages that we intend to deprecate should have a warning that pops
up when you load them. This is wrapped in a packageStartupMessage(), so
you can shut this off if it bothers you, but we want you to know that
you need to migrate to the newer sqlite versions of these packages.
Also on the deprecation block are KEGG and GO. Some people have asked
what to do if they want to use the GO to entrez gene ID mappings that
have been left out of the newer GO.db package. If you like these
mappings you should plan to use an appropriate organism level package.
Here are the names of some organism level packages:
For human = org.Hs. eg.db
For mouse = org.Mm.eg.db
For rat = org.Rn.eg.db
For yeast = org.Sc.sgd.db
For fly = org.Dm.eg.db
Please note that the annotation packages now have some new stuff in them
that you may not have noticed before such as ensemble accessions. This
is especially true for the organism level packages where we sometimes
will put additional species specific information such as flybase IDs.
I hope these help you.
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