Is there a reason one of the existing annotations provided in AnnotationHub cannot be used?
> library(AnnotationHub) > ah = AnnotationHub() qusnapshotDate(): 2018-08-01 > query(ah, "Chlamydomonas_reinhardtii") AnnotationHub with 2 records # snapshotDate(): 2018-08-01 # $dataprovider: Inparanoid8, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ # $species: Chlamydomonas reinhardtii # $rdataclass: Inparanoid8Db, OrgDb # additional mcols(): taxonomyid, genome, description, # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, # rdatapath, sourceurl, sourcetype # retrieve records with, e.g., 'object[["AH10477"]]' title AH10477 | hom.Chlamydomonas_reinhardtii.inp8.sqlite AH62519 | org.Chlamydomonas_reinhardtii.eg.sqlite Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Bijie Ren <b3...@ucsd.edu> Sent: Wednesday, August 1, 2018 1:50:10 PM To: bioc-devel@r-project.org Subject: EXTERNAL: [Bioc-devel] SQLForge Question about creating a new species package for Chlamydomonas reinhardtii Dear all, I wanna create a new annotation package for Chlamydomonas reinhardtii. However, sequencing data in NCBI for this species is not updated while there's a updated version of genome information and annotation in Phytozyome. I'm wondering can I use phytozome ID as an input to create such annotation package in R for WGCNA? If so will SQLForge use them to compare with intermediate? Best Regards, Bijie Ren [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel 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. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
