GitHub - waldronlab/bugsigdbr: R-side access to published microbial signatures from BugSigDB (original) (raw)

bugsigdbr

Lifecycle: experimental R-CMD-check-bioc Codecov test coverage

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

Installation instructions

Get the latest stable R release fromCRAN. Then install bugsigdbr fromBioconductor using the following code:

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

BiocManager::install("bugsigdbr")

Or the development version fromGitHub 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.