Read/Write, Transform, and Summarize 'BIOM' Data

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.


Reference manual

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1.0.2 by Daniel P. Smith, a year ago

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Authors: Daniel P. Smith [aut, cre, cph]

Documentation:   PDF Manual  

AGPL-3 license

Imports magrittr, methods, plyr, Rcpp, RcppParallel, R.utils, rjson, slam, openxlsx

Suggests ape, reshape2, rhdf5, testthat

Linking to Rcpp, RcppParallel

See at CRAN