bugphyzz
A harmonized data resource and software for enrichment analysis of microbial physiologies
Bioconductor version: 3.23 · Package version: 1.6.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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
| Maintainer | Samuel Gamboa <Samuel.Gamboa.Tuz@gmail.com> |
| Author | Samuel 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] |
| License | Artistic-2.0 |
| URL | https://github.com/waldronlab/bugphyzz |
| Bug Reports | https://github.com/waldronlab/bugphyzz/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ExperimentData, MicrobiomeData, ReproducibleResearch |
| Package Short Url | https://bioconductor.org/packages/bugphyzz/ |
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.
Download
Follow the installation instructions to use this package in your R session.
| Source package | bugphyzz_1.6.0.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