very interesting development, we have several folks who will take a look. FYI
%vjcair> R CMD INSTALL greeng*b Bioconductor version 3.2 (BiocInstaller 1.19.9), ?biocLite for help Loading required package: digest Loading required package: tools Loading required package: utils Loading required package: codetools * installing to library ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library’ * installing *source* package ‘greengenes13.5MgDb’ ... ** R ** preparing package for lazy loading Warning in .recacheSubclasses(def@className, def, doSubclasses, env) : undefined subclass "externalRefMethod" of class "functionORNULL"; definition not updated ** help No man pages found in package ‘greengenes13.5MgDb’ *** installing help indices ** building package indices ** testing if installed package can be loaded Bioconductor version 3.2 (BiocInstaller 1.19.9), ?biocLite for help Loading required package: digest Loading required package: tools Loading required package: utils Loading required package: codetools Warning in .recacheSubclasses(def@className, def, doSubclasses, env) : undefined subclass "externalRefMethod" of class "functionORNULL"; definition not updated /gg_13_5.fasta.gz: Permission denied On Tue, Aug 4, 2015 at 9:43 AM, Nathan Olson <nathandavidol...@gmail.com> wrote: > We are starting to work on an infrastructure for annotation of 16S > metagenomic sequencing datasets and would like your comments and/or > contributions. Below are links to two github repositories: > metagenomeFeatures and greengenes13.5MgDb. The metagenomeFeatures package > contains two classes; mgDb, for 16S sequence databases, and > metagenomeAnnotation, for annotating a sequence dataset with taxonomic > information from a mgDb object. The greengenes13.5MgDb package, loads a > mgDb object with the greengenes 13.5 database. greengenes 13.5 was used as > an example database, we plan on adding additional packages for other > commonly used databases, e.g RDP and Silva. > > The metagenomeFeatures includes two vignettes to demonstrating the mgDb and > metagenomeAnnotation class methods using the greengenes13.5MgDb as an > example database. > > We are planning on adding additional methods for the mgDb and > metagenomeAnnotation classes. For the mgDb class, assigning query > sequences to database sequences using rRDP classifier, and/or sequence > alignment methods that are part of the Biostrings package. For the > metagenomeAnnotation class we plan to include the ability to create a > phylogenetic tree from a metagenomeAnnotation object. > We would appreciate comments on the package and suggestions for additional > features. > > Links to package github repositories > > https://github.com/HCBravoLab/metagenomeFeatures > > https://github.com/HCBravoLab/greengenes13.5MgDb > > Thanks > > Nate Olson and Hector Corrada Bravo > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
