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bugsigdbr

R-side access to published microbial signatures from BugSigDB


Bioconductor version: Release (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")

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 1.8.4
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.1)
Imports BiocFileCache, methods, 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_1.8.4.tar.gz
Windows Binary bugsigdbr_1.8.4.zip (64-bit only)
macOS Binary (x86_64) bugsigdbr_1.8.4.tgz
macOS Binary (arm64) bugsigdbr_1.8.4.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
Old Source Packages for BioC 3.18 Source Archive