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 (3.18)

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 (from within R, enter citation("bugsigdbr")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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	PDF
NEWS	Text

Details

biocViews	DataImport, GeneSetEnrichment, Metagenomics, Microbiome, Software
Version	1.7.5
In Bioconductor since	BioC 3.14 (R-4.1) (2 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	BiocFileCache, methods, vroom, utils
Linking To
Suggests	BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>= 3.0.0)
System Requirements
Enhances
URL	https://github.com/waldronlab/bugsigdbr
Bug Reports	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_1.7.5.tar.gz
Windows Binary	bugsigdbr_1.7.5.zip
macOS Binary (x86_64)	bugsigdbr_1.7.5.tgz
macOS Binary (arm64)	bugsigdbr_1.7.5.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