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:
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.
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 H0: 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.