This repo demonstrates several analyses of curated microbe signatures from https://bugsigdb.org. See "Articles" for existing analyses, and "Reference" for functions provided by this packages.
bugSigSimple requires Bioconductor version 3.14 or later:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install()
BiocManager::version()To install this bugSigSimple and use these functions, do:
BiocManager::install("remotes", dependencies = TRUE)
BiocManager::install("waldronlab/bugSigSimple", dependencies = TRUE)- Delivery Mode and the Meconium Microbiome by Shaimaa Elsafoury for a basic creation of a study table and tables of the frequency of the most commonly identified taxa.
- The COVID-19 associated microbiome by Clare Grieve: for professional tables, clustered heatmaps and interactive heatmaps for identifying similar signatures, and hierarchical dendrograms.
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An analysis of Most frequent taxa in Major Depression and Bipolar Disorder by Fatima Azhar: This analysis does not take advantage of current functionality provided by this package and by BugSigDBStats, but it demonstrates a manual binomial test that can be used to test
$H_0$ : a taxon is equally probable to be reported as increased abundance or decreased abundance. This is only a sufficiently powered test when the same taxon is reported in at least 6 different studies (binom.test(0, 6) -> p=0.03125)) - The Irritable Bowel Syndrome-associated Microbiome by Kweku Amoo: Similar to 1 in another context.
- The Endometriosis-associated Microbiome by Samara Khan: This analysis generates a hypothesis based on frequently identified genera in bugsigdb.org, then tests the hypothesis with individual-participant data from curatedMetagenomicData, using linear regression, t-test, a Poisson model, and (zero-inflated) negative binomial log-linear models.
- Analysis of prevalent stool genera in bugsigdb.org by Haoyan Zhong: This analysis utilizes a set of signatures of prevalent species and genera found in healthy human microbiomes (https://bugsigdb.org/Study_562) for overlap with other signatures in bugsigdb.org. It focuses on gut microbiome signatures, but there are signatures of healthy prevalent genera and species available for other body sites as well.
- 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 releses 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 channel