bugphyzz

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20

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

Bioconductor version: Release (3.23)

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")):

Samuel Gamboa, Levi Waldron, Kelly Eckenrode, Jonathan Ye, Jennifer Wokaty. bugphyzz: A harmonized data resource and software for enrichment analysis of microbial physiologies. doi:10.18129/B9.bioc.bugphyzz, R package version 1.6.0, https://bioconductor.org/packages/bugphyzz.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	1.6.0
In Bioconductor since	BioC 3.20 (R-4.4) (2 years)
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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	bugphyzz_1.6.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-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/
Package Downloads Report	Download Stats