[Bioc-devel] Request for comment metagenomeFeatures package

[Vincent Carey]

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 at 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 at 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 <nathandavidolson at 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
>
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