rbiom-package: rbiom: Read/Write, Transform, and Summarize BIOM Data

In cmmr/rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data

rbiom: Read/Write, Transform, and Summarize BIOM Data

Description

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.

Multithreading

Many 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 RcppParallel's numThreads option. For instance:

    RcppParallel::setThreadOptions(numThreads = 4)

Author(s)

Maintainer: Daniel P. Smith [e-mail] (ORCID)

Other contributors:

• Alkek Center for Metagenomics and Microbiome Research [copyright holder, funder]

See Also

Useful links:

• https://cmmr.github.io/rbiom/

• https://github.com/cmmr/rbiom

• Report bugs at https://github.com/cmmr/rbiom/issues

cmmr/rbiom documentation built on April 28, 2024, 6:38 a.m.