Name: MMUPHin
User manual || Tutorial
Description: MMUPHin is a Bioconductor package implementing meta-analysis methods for microbial community profiles. It has interfaces for: a) covariate-controlled batch and study effect adjustment, b) meta-analytic differential abundance testing, and meta-analytic discovery of c) discrete (cluster-based) or d) continuous unsupervised population structure.
Overall, MMUPHin enables the normalization and combination of multiple microbial community studies. It can then help in identifying microbes, genes, or pathways that are differential with respect to combined phenotypes. Finally, it can find clusters or gradients of sample types that reproduce consistently among studies.
Citation
A manuscript describing MMUPHin , with its application in a collection of inflammatory bowel disease studies is currently in preparation:
Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier, Curtis Huttenhower Population Structure Discovery in Meta-Analyzed Microbial Communities and Inflammatory Bowel Disease.
In the meantime, if you use MMUPHin in your work, please cite the package itself (from within R, enter citation("MMUPHin") ):
Ma S (2019). MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies. R package version 0.99.3.