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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../../data/experiment/html/bugphyzz.html below:

Bioconductor - bugphyzz (development version)

bugphyzz

This is the development version of bugphyzz; for the stable release version, see bugphyzz.

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

Bioconductor version: Development (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: 0000-0002-6863-7943 , Levi Waldron [aut] 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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews ExperimentData, MicrobiomeData, ReproducibleResearch Version 1.3.0 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 See More Suggests DT, forcats, ggplot2, htmltools, knitr, rmarkdown, sessioninfo, testthat, EnrichmentBrowser, MicrobiomeBenchmarkData, mia, stats, rlang, limma, mgsub, methods, readr, crayon, tibble, magrittr, tidytext, BiocStyle Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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