Package: POMS 1.0.1

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>.

Authors:Gavin Douglas [aut, cre]

POMS_1.0.1.tar.gz
POMS_1.0.1.zip(r-4.7-any)POMS_1.0.1.zip(r-4.6-any)POMS_1.0.1.zip(r-4.5-any)
POMS_1.0.1.tgz(r-4.6-any)POMS_1.0.1.tgz(r-4.5-any)
POMS_1.0.1.tar.gz(r-4.7-any)POMS_1.0.1.tar.gz(r-4.6-any)
POMS_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
POMS/json (API)

# Install 'POMS' in R:
install.packages('POMS', repos = c('https://gavinmdouglas.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gavinmdouglas/poms/issues

On CRAN:

Conda:

3.95 score 18 stars 4 scripts 249 downloads 11 exports 29 dependencies

Last updated from:f1eca60b65. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK112
source / vignettesOK171
linux-releaseOK106
macos-releaseOK189
macos-oldrelOK192
windows-develOK65
windows-releaseOK66
windows-oldrelOK65
wasm-releaseOK106

Exports:abun_isometric_log_ratioscompute_node_balancesfilter_rare_table_colsgenome_content_phylo_regressnode_taxaphylolm_summaryPOMS_pipelineprep_func_node_infoprevalence_norm_logitspecificity_scoressubset_by_col_and_filt

Dependencies:apeclicodetoolscpp11data.tabledigestfastmatchfuturefuture.applygenericsglobalsglueigraphlatticelifecyclelistenvmagrittrMASSMatrixnlmeparallellyphangornphylolmpkgconfigquadprogRcpprlangvctrsXNomial