Package: bugsigdbr 1.19.0

Ludwig Geistlinger

bugsigdbr: R-side access to published microbial signatures from BugSigDB

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.

Authors:Ludwig Geistlinger [aut, cre], Jennifer Wokaty [aut], Levi Waldron [aut], NCI [fnd]

bugsigdbr_1.19.0.tar.gz
bugsigdbr_1.19.0.zip(r-4.7)bugsigdbr_1.19.0.zip(r-4.6)bugsigdbr_1.19.0.zip(r-4.5)
bugsigdbr_1.19.0.tgz(r-4.6-any)bugsigdbr_1.19.0.tgz(r-4.5-any)
bugsigdbr_1.19.0.tar.gz(r-4.7-any)bugsigdbr_1.19.0.tar.gz(r-4.6-any)
bugsigdbr_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bugsigdbr/json (API)

# Install 'bugsigdbr' in R:

install.packages('bugsigdbr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

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

On BioConductor:bugsigdbr-1.19.0(bioc 3.24)bugsigdbr-1.18.0(bioc 3.23)

dataimport genesetenrichment metagenomics microbiome bioconductor-package r01ca230551

6.93 score 6 stars 68 scripts 814 downloads 10 exports 43 dependencies

Last updated from:5d737b3413. Checks:7 NOTE, 2 OK, 1 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	138
linux-devel-x86_64	NOTE	325
source / vignettes	OK	241
linux-release-x86_64	ERROR	341
macos-release-arm64	NOTE	225
macos-oldrel-arm64	NOTE	270
windows-devel	NOTE	277
windows-release	NOTE	258
windows-oldrel	NOTE	238
wasm-release	OK	108

Exports:browseSignature browseTaxon extractTaxLevel getMetaSignatures getOntology getSignatures importBugSigDB restrictTaxLevel subsetByOntology writeGMT

Dependencies:askpass BiocFileCache bit bit64 blob cachem cli cpp11 crayon curl DBI dbplyr dplyr fastmap filelock generics glue hms httr2 lifecycle magrittr memoise openssl pillar pkgconfig prettyunits progress purrr R6 rappdirs rlang RSQLite stringi stringr sys tibble tidyr tidyselect tzdb utf8 vctrs vroom withr

R-side access to published microbial signatures from BugSigDB

BugSigDB: a comprehensive database of published microbial signatures | Obtaining published microbial signatures from BugSigDB | Extracting microbe signatures | Writing microbe signatures to file in GMT format | Displaying BugSigDB signature and taxon pages | Ontology-based queries for experimental factors and body sites | Session info

Rendered frombugsigdbr.Rmdusingknitr::rmarkdown

Last update: 2025-12-29
Started: 2021-04-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Displaying BugSigDB signatures pages in a web browser	browseSignature
Displaying BugSigDB taxon pages in a web browser	browseTaxon
Extract specific taxonomic levels from a microbe signature	extractTaxLevel
Obtain meta-signatures for a column of interest	getMetaSignatures
Obtain the EFO and UBERON ontology	getOntology
Obtain microbe signatures from BugSigDB	getSignatures
Obtain published microbial signatures from bugsigdb.org	importBugSigDB
Restrict microbe signatures to specific taxonomic levels	restrictTaxLevel
Ontology-based subsetting of BugSigDB signatures	subsetByOntology
Write microbe signatures to file in GMT format	writeGMT