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
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]
, Levi Waldron [aut]
, Kelly Eckenrode [aut], Jonathan Ye [aut], Jennifer Wokaty [aut]
Maintainer: Samuel Gamboa <Samuel.Gamboa.Tuz at gmail.com>
citation("bugphyzz")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, MicrobiomeData, ReproducibleResearch |
| Version | 1.6.0 |
| 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.
| 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 |