Package: bugsigdbr 1.11.0

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]

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bugsigdbr.pdf |bugsigdbr.html✨
bugsigdbr/json (API)
NEWS

# 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-1.11.0(bioc 3.20)bugsigdbr-1.10.0(bioc 3.19)

bioconductor-package

10 exports 1.58 score 46 dependencies

Last updated 2 months agofrom:1d70990be4

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 fansi fastmap filelock generics glue hms httr jsonlite lifecycle magrittr memoise mime openssl pillar pkgconfig plogr prettyunits progress purrr R6 rlang RSQLite stringi stringr sys tibble tidyr tidyselect tzdb utf8 vctrs vroom withr

R-side access to published microbial signatures from BugSigDB

Ludwig Geistlinger, Jennifer Wokaty, and Levi Waldron

Rendered frombugsigdbr.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-06-28
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