mina

DOI: 10.18129/B9.bioc.mina    

This is the development version of mina; for the stable release version, see mina.

Microbial community dIversity and Network Analysis

Bioconductor version: Development (3.15)

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>

Citation (from within R, enter citation("mina")):

Installation

To install this package, start R (version "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 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
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_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) mina_1.3.0.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

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