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-4.5)POMS_1.0.1.zip(r-4.4)POMS_1.0.1.zip(r-4.3)
POMS_1.0.1.tgz(r-4.4-any)POMS_1.0.1.tgz(r-4.3-any)
POMS_1.0.1.tar.gz(r-4.5-noble)POMS_1.0.1.tar.gz(r-4.4-noble)
POMS_1.0.1.tgz(r-4.4-emscripten)POMS_1.0.1.tgz(r-4.3-emscripten)
POMS.pdf |POMS.html✨
POMS/json (API)

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

Peer review:

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

On CRAN:

3.98 score 19 stars 4 scripts 235 downloads 11 exports 29 dependencies

Last updated 2 years agofrom:f1eca60b65. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winOKNov 19 2024
R-4.5-linuxOKNov 19 2024
R-4.4-winOKNov 19 2024
R-4.4-macOKNov 19 2024
R-4.3-winOKNov 19 2024
R-4.3-macOKNov 19 2024

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