bugphyzz

This is the released version of bugphyzz; for the devel version, see bugphyzz.

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

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DOI: 10.18129/B9.bioc.bugphyzz

Bioconductor version: Release (3.22)

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.

Author: Samuel Gamboa [aut, cre] ORCID iD ORCID: 0000-0002-6863-7943 , Levi Waldron [aut] ORCID iD ORCID: 0000-0003-2725-0694 , Kelly Eckenrode [aut], Jonathan Ye [aut], Jennifer Wokaty [aut]

Maintainer: Samuel Gamboa <Samuel.Gamboa.Tuz at gmail.com>

Citation (from within R, enter citation("bugphyzz")):

Installation

To install this package, start R (version "4.5") and enter:


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

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("bugphyzz")

bugphyzz HTML R Script

Sources HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ExperimentData, MicrobiomeData, ReproducibleResearch

Version 1.4.0

License Artistic-2.0

Depends R (>= 4.4)

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

System Requirements

URL https://github.com/waldronlab/bugphyzz

Bug Reports https://github.com/waldronlab/bugphyzz/issues

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

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package bugphyzz_1.4.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/bugphyzz

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bugphyzz

Package Short Url https://bioconductor.org/packages/bugphyzz/

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