bugsigdbr
This is the development version of bugsigdbr; for the stable release version, see bugsigdbr.
R-side access to published microbial signatures from BugSigDB
Bioconductor version: Development (3.24)
The bugsigdbr package implements convenient access to bugsigdb.org from within R/Bioconductor. The goal of the package is to facilitate import of BugSigDB data into R/Bioconductor, provide utilities for extracting microbe signatures, and enable export of the extracted signatures to plain text files in standard file formats such as GMT.
Author: Ludwig Geistlinger [aut, cre], Jennifer Wokaty [aut], Levi Waldron [aut], NCI [fnd] (GrantNo.: R01CA230551)
Maintainer: Ludwig Geistlinger <ludwig.geistlinger at gmail.com>
citation("bugsigdbr")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("bugsigdbr")
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("bugsigdbr")| R-side access to BugSigDB | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, GeneSetEnrichment, Metagenomics, Microbiome, Software |
| Version | 1.19.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1) |
| Imports | BiocFileCache, methods, vroom, utils |
| System Requirements | |
| URL | https://github.com/waldronlab/bugsigdbr |
| Bug Reports | https://github.com/waldronlab/bugsigdbr/issues |
See More
| Suggests | BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | TaxSEA |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | bugsigdbr_1.19.0.tar.gz |
| Windows Binary (x86_64) | bugsigdbr_1.19.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | bugsigdbr_1.19.0.tgz |
| macOS Binary (sonoma-arm64) | bugsigdbr_1.19.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/bugsigdbr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/bugsigdbr |
| Bioc Package Browser | https://code.bioconductor.org/browse/bugsigdbr/ |
| Package Short Url | https://bioconductor.org/packages/bugsigdbr/ |
| Package Downloads Report | Download Stats |