A toolkit for working with Biological Observation Matrix (BIOM) files. Features include reading/writing all BIOM formats, rarefaction, alpha diversity, beta diversity (including UniFrac), summarizing counts by taxonomic level, and sample subsetting. Standalone functions for reading, writing, and subsetting phylogenetic trees are also provided. All CPU intensive operations are encoded in C with multi-thread support.
rbiom functions support multithreading:
The default behavior of these function is to run on as many cores as are
available in the local compute environment. If you wish to limit the number
of simultaneous threads, set the
rbiom.max.threads option. For
options('rbiom.max.threads' = 6)
Alternatively, you can register a custom parallel backend, which will be
detected and used for multithreaded functions. Please note that only the
doSNOW backend currently supports progress tracking. With other
backends, you will only be notified of the beginning and ending of computations.
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