mina
Microbial community dIversity and Network Analysis
Bioconductor version: Release (3.19)
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("mina")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("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")| Microbial dIversity and Network Analysis with MINA | HTML | R Script |
| Reference Manual |
Details
| biocViews | Software, WorkflowStep |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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 |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/Guan06/mina |
See More
| Suggests | knitr, rmarkdown |
| Linking To | Rcpp, RcppParallel, RcppArmadillo |
| Enhances | doMC |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | mina_1.12.0.tar.gz |
| Windows Binary (x86_64) | mina_1.12.0.zip |
| macOS Binary (x86_64) | mina_1.12.0.tgz |
| macOS Binary (arm64) | mina_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/mina |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/mina |
| Bioc Package Browser | https://code.bioconductor.org/browse/mina/ |
| Package Short Url | https://bioconductor.org/packages/mina/ |
| Package Downloads Report | Download Stats |