Hi, This is a heads up about a few changes we've made to the production of in-house annotations for Bioconductor 3.3.
# Microarray packages: We will propagate but no longer rebuild the ChipDb, probe and cdf packages. These data have been static for some time. The packages will continue to be available in future releases as the same version they are in the current devel branch. # KEGG.db KEGG.db will be propagated at the same version and not rebuilt. KEGG went commercial several years ago and the alternative is the REST interface in KEGGREST. # Inparanoid The Inparanoid packages will be propagated at the same version and not rebuilt: http://www.bioconductor.org/packages/release/BiocViews.html#___InparanoidDb The last data release was 2007. Is there interest in using homologene (http://www.ncbi.nlm.nih.gov/homologene) as a replacement? Those data are 'new' as of May 2014. # db0, OrgDb, PFAM.db and GO.db Nothing special here, just rebuilt them. # TxDb The only track modified since last release was TxDb.Rnorvegicus.UCSC.rn5.refGene so that was updated. We've added a few new TxDbs (refGene track) in the interest of supplying compatible cross coverage of BSgenome, TxDb and OrgDb packages. These are the building blocks of the OrganismDb packages and we plan to make use of them after the release. Bioconductor 3.3 will host compatible BSgenome, TxDb and OrgDb packages for these organisms: human: hg38 chimp: panTro4 cow: bostau8 worm: ce11 dog: canFam3 fly: dm6 zebrafish: danRer10 chicken: galGal4 rhesus: rheMac3 mouse: mm10 rat: rn6 yeast: sacCer3 pig: susScr3 # BSgenome, SNPlocs, XSNPlocs Herve added BSgenome packages for danRer10, taeGut2 and ce11. He also added these two contributed by Timothée Flutre: BSgenome.Vvinifera.URGI.IGGP12Xv0 BSgenome.Vvinifera.URGI.IGGP12Xv2 # OrganismDb We currently host 3 of these for human, mouse and rat. The packages don't contain data but instead point to GO.db and a compatible TxDb/OrgDb pair and for this reason don't need to be updated. We plan on actively developing this family after the release so no new packages of this type were generated fro Bioconductor 3.3. This is my first go-round at producing the annotation packages and they are now in the devel branch. If you see anything strange or inconsistent please let me know asap so I can fix before the release. Thanks. Valerie This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
