mina

DOI: 10.18129/B9.bioc.mina    

Microbial community dIversity and Network Analysis

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("mina")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("mina")

 

HTML	R Script	Microbial dIversity and Network Analysis with MINA
PDF		Reference Manual

Details

biocViews	Software, WorkflowStep
Version	1.0.0
In Bioconductor since	BioC 3.13 (R-4.1) (< 6 months)
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
SystemRequirements
Enhances	doMC
URL
BugReports	https://github.com/Guan06/mina
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	mina_1.0.0.tar.gz
Windows Binary	mina_1.0.0.zip
macOS 10.13 (High Sierra)	mina_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mina
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mina
Package Short Url	https://bioconductor.org/packages/mina/
Package Downloads Report	Download Stats