POMS: Phylogenetic Organization of Metagenomic Signals

Code to identify functional enrichments across diverse taxa in phylogenetic tree, particularly where these taxa differ in abundance across samples in a non-random pattern. The motivation for this approach is to identify microbial functions encoded by diverse taxa that are at higher abundance in certain samples compared to others, which could indicate that such functions are broadly adaptive under certain conditions. See 'GitHub' repository for tutorial and examples: <https://github.com/gavinmdouglas/POMS/wiki>. Citation: Gavin M. Douglas, Molly G. Hayes, Morgan G. I. Langille, Elhanan Borenstein (2022) <doi:10.1093/bioinformatics/btac655>.

Version: 1.0.1
Depends: R (≥ 3.5.0)
Imports: ape (≥ 3.0), data.table, MASS, parallel (≥ 3.3.0), phangorn (≥ 2.0.0), phylolm (≥ 2.6), utils, XNomial (≥ 1.0.4)
Suggests: testthat (≥ 3.0.0)
Published: 2022-12-14
Author: Gavin Douglas [aut, cre]
Maintainer: Gavin Douglas <gavinmdouglas at gmail.com>
License: GPL-3
NeedsCompilation: no
Citation: POMS citation info
Materials: README
CRAN checks: POMS results

Documentation:

Reference manual: POMS.pdf

Downloads:

Package source: POMS_1.0.1.tar.gz
Windows binaries: r-devel: POMS_1.0.1.zip, r-release: POMS_1.0.1.zip, r-oldrel: POMS_1.0.1.zip
macOS binaries: r-release (arm64): POMS_1.0.1.tgz, r-oldrel (arm64): POMS_1.0.1.tgz, r-release (x86_64): POMS_1.0.1.tgz

Linking:

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