bugsigdbr
R-side access to published microbial signatures from BugSigDB
Bioconductor version: Release (3.20)
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]
Maintainer: Ludwig Geistlinger <ludwig.geistlinger at gmail.com>
citation("bugsigdbr")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.12.0 |
In Bioconductor since | BioC 3.14 (R-4.1) (3 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 | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | bugsigdbr_1.12.0.tar.gz |
Windows Binary (x86_64) | bugsigdbr_1.12.0.zip |
macOS Binary (x86_64) | bugsigdbr_1.12.0.tgz |
macOS Binary (arm64) | bugsigdbr_1.11.4.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 |