yusufipektas / bugsigdbr

R-side access to published microbial signatures from BugSigDB

bugsigdbr

Utilities for accessing data from BugSigDB.org and creating plain text signatures.

Installation instructions

Get the latest stable R release from CRAN. Then install bugsigdbr from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("bugsigdbr")

Or the development version from GitHub with:

BiocManager::install("waldronlab/bugsigdbr")

Example

library(bugsigdbr)
bsdb <- bugsigdbr::importBugSigDB()

Citation

Ludwig Geistlinger, Chloe Mirzayi, Fatima Zohra, Rimsha Azhar, Shaimaa Elsafoury, Clare Grieve, Jennifer Wokaty, Samuel David Gamboa-Tuz, Pratyay Sengupta, Isaac Hecht, Aarthi Ravikrishnan, Rafael S. Goncalves, Eric Franzosa, Karthik Raman, Vincent Carey, Jennifer B. Dowd, Heidi E. Jones, Sean Davis, Nicola Segata, Curtis Huttenhower, Levi Waldron (2023) BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures. Nature Biotechnology, doi: 10.1038/s41587-023-01872-y.

Useful links

• bugsigdb.org: A Comprehensive Database of Published Microbial Signatures
• BugSigDB issue tracker: Report bugs or feature requests for bugsigdb.org
• BugSigDBExports: Hourly data exports of bugsigdb.org
• Stable data releases: Periodic manually-reviewed stable data releases on Zenodo
• bugsigdbr: R/Bioconductor access to published microbial signatures from BugSigDB
• Curation issues: Report curation issues, requests studies to be added
• bugSigSimple: Simple analyses of BugSigDB data in R
• BugSigDBStats: Statistics and trends of BugSigDB
• BugSigDBPaper: Reproduces analyses of the Nature Biotechnology publication
• community-bioc Slack Team: Join #bugsigdb slack channel