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bugphyzz

A harmonized data resource and software for enrichment analysis of microbial physiologies

Bioconductor version: 3.24 · Package version: 1.7.1

bugphyzz is an electronic database of standardized microbial annotations. It facilitates the creation of microbial signatures based on shared attributes, which are utilized for bug set enrichment analysis. The data also includes annotations imputed with ancestra state reconstruction methods.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("bugphyzz")

Details

MaintainerSamuel Gamboa <Samuel.Gamboa.Tuz@gmail.com>
AuthorSamuel Gamboa [aut, cre] (ORCID: <https://orcid.org/0000-0002-6863-7943>), Levi Waldron [aut] (ORCID: <https://orcid.org/0000-0003-2725-0694>), Kelly Eckenrode [aut], Jonathan Ye [aut], Jennifer Wokaty [aut], NCI [fnd] (GrantNo.: R01CA230551)
LicenseArtistic-2.0
URLhttps://github.com/waldronlab/bugphyzz
Bug Reportshttps://github.com/waldronlab/bugphyzz/issues
Downloads rank125
Source branchdevel
biocViewsExperimentData, MicrobiomeData, ReproducibleResearch

Download

Follow the installation instructions to use this package in your R session.

Source packagebugphyzz_1.7.1.tar.gz
Dependencies

Depends: R (>= 4.4)

Imports: dplyr, utils, purrr, stringr, tidyr, tidyselect, BiocFileCache, httr2, tools, S4Vectors

Suggests: DT, forcats, ggplot2, htmltools, knitr, rmarkdown, sessioninfo, testthat, EnrichmentBrowser, MicrobiomeBenchmarkData, mia, stats, rlang, limma, mgsub, methods, readr, crayon, tibble, magrittr, tidytext, BiocStyle