DOI: 10.18129/B9.bioc.mina  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see mina.

Microbial community dIversity and Network Analysis

Bioconductor version: 3.16

An increasing number of microbiome datasets have been generated and analyzed with the help of rapidly developing sequencing technologies. At present, analysis of taxonomic profiling data is mainly conducted using composition-based methods, which ignores interactions between community members. Besides this, a lack of efficient ways to compare microbial interaction networks limited the study of community dynamics. To better understand how community diversity is affected by complex interactions between its members, we developed a framework (Microbial community dIversity and Network Analysis, mina), a comprehensive framework for microbial community diversity analysis and network comparison. By defining and integrating network-derived community features, we greatly reduce noise-to-signal ratio for diversity analyses. A bootstrap and permutation-based method was implemented to assess community network dissimilarities and extract discriminative features in a statistically principled way.

Author: Rui Guan [aut, cre], Ruben Garrido-Oter [ctb]

Maintainer: Rui Guan <guan at mpipz.mpg.de>

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biocViews Software, WorkflowStep
Version 1.6.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License GPL
Depends R (>= 4.0.0)
Imports methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory, foreach, ggplot2, parallel, parallelDist, reshape2, plyr, biganalytics, stringr, Hmisc, utils
LinkingTo Rcpp, RcppParallel, RcppArmadillo
Suggests knitr, rmarkdown
Enhances doMC
BugReports https://github.com/Guan06/mina
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