rbiom: 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.

Version: 1.0.3
Depends: R (≥ 3.5.0)
Imports: magrittr, methods, plyr, Rcpp, RcppParallel, rjson, rlang, R.utils, slam, openxlsx
LinkingTo: Rcpp, RcppParallel
Suggests: ape, reshape2, rhdf5, testthat
Published: 2021-11-05
DOI: 10.32614/CRAN.package.rbiom
Author: Daniel P. Smith ORCID iD [aut, cre, cph]
Maintainer: Daniel P. Smith <dansmith at orst.edu>
BugReports: https://github.com/cmmr/rbiom/issues
License: AGPL-3
URL: https://cmmr.github.io/rbiom/index.html
NeedsCompilation: yes
Materials: README NEWS
CRAN checks: rbiom results


Reference manual: rbiom.pdf


Package source: rbiom_1.0.3.tar.gz
Windows binaries: r-devel: rbiom_1.0.3.zip, r-release: rbiom_1.0.3.zip, r-oldrel: rbiom_1.0.3.zip
macOS binaries: r-release (arm64): rbiom_1.0.3.tgz, r-oldrel (arm64): rbiom_1.0.3.tgz, r-release (x86_64): rbiom_1.0.3.tgz, r-oldrel (x86_64): rbiom_1.0.3.tgz
Old sources: rbiom archive


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