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)POMS_1.0.1.zip(r-4.6)POMS_1.0.1.zip(r-4.5)
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✨
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 199 downloads 11 exports 29 dependencies

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

TargetResultTimeFilesSyslog
linux-devel-x86_64OK122
source / vignettesOK162
linux-release-x86_64OK122
macos-release-arm64OK166
macos-oldrel-arm64OK146
windows-develOK81
windows-releaseOK76
windows-oldrelOK71
wasm-releaseOK126

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