Package: mina
Title: Microbial community dIversity and Network Analysis
Version: 1.19.0
Authors@R: c(person("Rui", "Guan", email = "guan@mpipz.mpg.de", role = c("aut", "cre")),
    person("Ruben", "Garrido-Oter", email = "garridoo@mpipz.mpg.de", role = "ctb"))
Description: 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.
Depends: R (>= 4.0.0)
LinkingTo: Rcpp, RcppParallel, RcppArmadillo
License: GPL
Encoding: UTF-8
Imports: methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory,
        foreach, ggplot2, parallel, parallelDist, reshape2, plyr,
        biganalytics, stringr, Hmisc, utils
LazyData: true
Suggests: knitr, rmarkdown
Enhances: doMC
VignetteBuilder: knitr
RoxygenNote: 7.1.1
Collate: 'RcppChk.R' 'RcppExports.R' 'all_classes.R' 'all_generics.R'
        'adj.R' 'all_accessors.R' 'bs_pm.R' 'check.R' 'com_dis.R'
        'com_plot.R' 'com_r2.R' 'data.R' 'dmr.R' 'fit_tabs.R'
        'get_rep.R' 'net_cls.R' 'net_cls_tab.R' 'net_dis.R'
        'net_dis_indi.R' 'net_dis_pcoa.R' 'net_dis_plot.R'
        'net_grp_cmp.R' 'net_node_cmp.R' 'norm_tab.R'
biocViews: Software, WorkflowStep
BugReports: https://github.com/Guan06/mina
Config/pak/sysreqs: make libicu-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:04:54 UTC
RemoteUrl: https://github.com/bioc/mina
RemoteRef: HEAD
RemoteSha: 7f01d560b99a9d7428dbc49229ce6c04f09f74df
NeedsCompilation: yes
Packaged: 2025-10-30 07:28:00 UTC; root
Author: Rui Guan [aut, cre],
  Ruben Garrido-Oter [ctb]
Maintainer: Rui Guan <guan@mpipz.mpg.de>
Built: R 4.6.0; x86_64-w64-mingw32; 2025-10-30 07:30:27 UTC; windows
Archs: x64
