{ "_id": "6a1ed675b401979e7340ea4a", "Package": "mina", "Title": "Microbial community dIversity and Network Analysis", "Version": "1.21.0", "Authors@R": "c(person(\"Rui\", \"Guan\", email = \"guan@mpipz.mpg.de\", role = c(\"aut\", \"cre\")),\nperson(\"Ruben\", \"Garrido-Oter\", email = \"garridoo@mpipz.mpg.de\", role = \"ctb\"))", "Description": "An increasing number of microbiome datasets have been\ngenerated and analyzed with the help of rapidly developing\nsequencing technologies. At present, analysis of taxonomic\nprofiling data is mainly conducted using composition-based\nmethods, which ignores interactions between community members.\nBesides this, a lack of efficient ways to compare microbial\ninteraction networks limited the study of community dynamics.\nTo better understand how community diversity is affected by\ncomplex interactions between its members, we developed a\nframework (Microbial community dIversity and Network Analysis,\nmina), a comprehensive framework for microbial community\ndiversity analysis and network comparison. By defining and\nintegrating network-derived community features, we greatly\nreduce noise-to-signal ratio for diversity analyses. A\nbootstrap and permutation-based method was implemented to\nassess community network dissimilarities and extract\ndiscriminative features in a statistically principled way.", "License": "GPL", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "RoxygenNote": "7.1.1", "Collate": "'RcppChk.R' 'RcppExports.R' 'all_classes.R' 'all_generics.R'\n'adj.R' 'all_accessors.R' 'bs_pm.R' 'check.R' 'com_dis.R'\n'com_plot.R' 'com_r2.R' 'data.R' 'dmr.R' 'fit_tabs.R'\n'get_rep.R' 'net_cls.R' 'net_cls_tab.R' 'net_dis.R'\n'net_dis_indi.R' 'net_dis_pcoa.R' 'net_dis_plot.R'\n'net_grp_cmp.R' 'net_node_cmp.R' 'norm_tab.R'", "biocViews": "Software, WorkflowStep", "BugReports": "https://github.com/Guan06/mina", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:54:33 UTC", "RemoteUrl": "https://github.com/bioc/mina", "RemoteRef": "HEAD", "RemoteSha": "a79adb620856874ce9f258a7ddb55b5627793871", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-20 10:18:15 UTC", "User": "root" }, "Author": "Rui Guan [aut, cre],\nRuben Garrido-Oter [ctb]", "Maintainer": "Rui Guan ", "MD5sum": "59fcbc44a971152df546ff50c2608372", "_user": "bioc", "_type": "src", "_file": "mina_1.21.0.tar.gz", "_fileid": "9fad295357420713230b8fd156a8db4b9325b87fe0ccbdb023712285b4542395", "_filesize": 4416853, "_sha256": "9fad295357420713230b8fd156a8db4b9325b87fe0ccbdb023712285b4542395", "_created": "2026-05-20T10:18:15.000Z", "_published": "2026-06-02T13:11:17.191Z", "_jobs": [ { "job": 79077973984, "time": 176, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7107387497" }, { "job": 79077974128, "time": 298, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7107426934" }, { "job": 79077973917, "time": 293, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7107425020" }, { "job": 79077974164, "time": 273, "config": 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Return TRUE if they are NULL or both quantitative and descriptive files of same samples are included (i.e. the object is valid).", "topics": [ "check_mina" ] }, { "page": "check_mina_de", "title": "Check the object and return TRUE if the object includes descriptive table contains the same samples as quantitative table.", "topics": [ "check_mina_de" ] }, { "page": "check_mina_qu", "title": "Check the object and return TRUE if the object includes quantitative table.", "topics": [ "check_mina_qu" ] }, { "page": "cls_tab", "title": "Get the slot `cls_tab`.", "topics": [ "cls_tab" ] }, { "page": "com_dis", "title": "Calculate the community dissimilarity / distance matrix.", "topics": [ "com_dis" ] }, { "page": "com_dis_list", "title": "List of dissimilarity / distance supported in 'com_dis'. Dissimilarity / distance should be specified by exact string match.", "topics": [ "com_dis_list" ] }, { "page": "com_dis-matrix", "title": "Calculate the community dissimilarity / distance matrix of the input matrix.", "topics": [ "com_dis,matrix,ANY-method", "com_dis,matrix,character-method" ] }, { "page": "com_dis-mina", "title": "Calculate the community dissimilarity / distance matrix of `norm` with `mina` class object as input.", "topics": [ "com_dis,mina,ANY-method", "com_dis,mina,character-method" ] }, { "page": "com_plot", "title": "Visulization of components distance / dissimilarity in k dimension.", "topics": [ "com_plot" ] }, { "page": "com_plot-mina", "title": "Visulization of components distance / dissimilarity in k dimension.", "topics": [ "com_plot,mina,ANY-method", "com_plot,mina,character-method" ] }, { "page": "com_r2", "title": "Calculate the unexplained variance ratio using formula indicated in: Anderson, M.J. 2001. 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If `norm` table exist in the `mina` object, descriptive table will be filtered again to only keep samples present in `norm`.", "topics": [ "fit_tabs,mina-method" ] }, { "page": "get_net_cls_tab", "title": "Get the cluster table `cls_tab` from quantitative table `norm` and network clustering results `cls`.", "topics": [ "get_net_cls_tab" ] }, { "page": "get_net_cls_tab-matrix-data.frame-method", "title": "Get the cluster table `cls_tab` from quantitative table `norm` and network clustering results `cls`.", "topics": [ "get_net_cls_tab,matrix,data.frame-method" ] }, { "page": "get_r2", "title": "Same function as `com_r2` with matrix and corresponding descriptive table as input.", "topics": [ "get_r2" ] }, { "page": "get_r2-mat", "title": "Function for unexplained variance ratio calculation indicated in Anderson, M.J. 2001. A new method for non-parametric multivariate analysis of variance. 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Function for `tina` dissimilarity/distance calculation. Modified from Schmidt et al., 2016.", "topics": [ "tina" ] }, { "page": "tina-matrix-method", "title": "Function for `tina` dissimilarity calculation. Modified from Schmidt et al., 2016. 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