bugsigdbr

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see bugsigdbr.

R-side access to published microbial signatures from BugSigDB

Bioconductor version: 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 (!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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, GeneSetEnrichment, Metagenomics, Microbiome, Software

Version 1.0.1

In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)

License GPL-3

Depends R (>= 4.1)

Imports BiocFileCache, vroom, utils

System Requirements

URL https://github.com/waldronlab/bugsigdbr

Bug Reports https://github.com/waldronlab/bugsigdbr/issues

Suggests BiocStyle, knitr, 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_1.0.1.tar.gz

Windows Binary bugsigdbr_1.0.1.zip

macOS 10.13 (High Sierra) bugsigdbr_1.0.1.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 3.14 Source Archive