bugsigdbr

DOI: 10.18129/B9.bioc.bugsigdbr  

R-side access to published microbial signatures from BugSigDB

Bioconductor version: Release (3.16)

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 hms.harvard.edu>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	R-side access to BugSigDB
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, GeneSetEnrichment, Metagenomics, Microbiome, Software
Version	1.4.3
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	BiocFileCache, methods, vroom, utils
LinkingTo
Suggests	BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/waldronlab/bugsigdbr
BugReports	https://github.com/waldronlab/bugsigdbr/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	bugsigdbr_1.4.3.tar.gz
Windows Binary	bugsigdbr_1.4.3.zip
macOS Binary (x86_64)	bugsigdbr_1.4.3.tgz
macOS Binary (arm64)	bugsigdbr_1.4.3.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
Old Source Packages for BioC 3.16	Source Archive