bugsigdbr

DOI: 10.18129/B9.bioc.bugsigdbr    

This is the development version of bugsigdbr; to use it, please install the devel version of Bioconductor.

R-side access to published microbial signatures from BugSigDB

Bioconductor version: Development (3.14)

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>

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews DataImport, GeneSetEnrichment, Metagenomics, Microbiome, Software
Version 0.99.8
In Bioconductor since BioC 3.14 (R-4.1)
License GPL-3
Depends R (>= 4.1)
Imports BiocFileCache, vroom, utils
LinkingTo
Suggests BiocStyle, knitr, 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_0.99.8.tar.gz
Windows Binary bugsigdbr_0.99.8.zip
macOS 10.13 (High Sierra) bugsigdbr_0.99.8.tgz
Source Repository git clone https://git.bioconductor.org/packages/bugsigdbr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bugsigdbr
Package Short Url https://bioconductor.org/packages/bugsigdbr/
Package Downloads Report Download Stats

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