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  "Title": "Network Analysis for Omics Data",
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  "Description": "Comprehensive network analysis package. Calculate\ncorrelation network fastly, accelerate lots of analysis by\nparallel computing. Support for multi-omics data, search\nsub-nets fluently. Handle bigger data, more than 10,000 nodes\nin each omics. Offer various layout method for multi-omics\nnetwork and some interfaces to other software ('Gephi',\n'Cytoscape', 'ggplot2'), easy to visualize. Provide\ncomprehensive topology indexes calculation, including\necological network stability.",
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  "Date/Publication": "2026-05-24 02:15:00 UTC",
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  "Maintainer": "Chen Peng <bfzede@gmail.com>",
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    {
      "page": "anno_vertex",
      "title": "Use data.frame to annotate vertexes of metanet",
      "concept": [
        "manipulate"
      ],
      "topics": [
        "anno_node",
        "anno_vertex"
      ]
    },
    {
      "page": "arc_count",
      "title": "Edgelist",
      "topics": [
        "arc_count"
      ]
    },
    {
      "page": "arc_taxonomy",
      "title": "Edgelist",
      "topics": [
        "arc_taxonomy"
      ]
    },
    {
      "page": "as_arc",
      "title": "Layout as a arc",
      "concept": [
        "layout"
      ],
      "topics": [
        "as_arc"
      ]
    },
    {
      "page": "as_circle_tree",
      "title": "Layout as a circle_tree",
      "concept": [
        "layout"
      ],
      "topics": [
        "as_circle_tree"
      ]
    },
    {
      "page": "as_coors",
      "title": "Transfer to a coors object",
      "topics": [
        "as_coors"
      ]
    },
    {
      "page": "as_line",
      "title": "Layout as a line",
      "concept": [
        "layout"
      ],
      "topics": [
        "as_line"
      ]
    },
    {
      "page": "as_multi_layer",
      "title": "Layout as a multi_layer",
      "concept": [
        "layout"
      ],
      "topics": [
        "as_multi_layer"
      ]
    },
    {
      "page": "as_poly_sector",
      "title": "Layout as a multi_layer",
      "concept": [
        "layout"
      ],
      "topics": [
        "as_poly_sector"
      ]
    },
    {
      "page": "as_polyarc",
      "title": "Layout as a polyarc",
      "concept": [
        "layout"
      ],
      "topics": [
        "as_polyarc"
      ]
    },
    {
      "page": "as_polycircle",
      "title": "Layout as a polycircle",
      "concept": [
        "layout"
      ],
      "topics": [
        "as_polycircle"
      ]
    },
    {
      "page": "as_polygon",
      "title": "Layout as a polygon",
      "concept": [
        "layout"
      ],
      "topics": [
        "as_polygon"
      ]
    },
    {
      "page": "as.ggig",
      "title": "Transfer an igraph object to a ggig",
      "concept": [
        "plot"
      ],
      "topics": [
        "as.ggig"
      ]
    },
    {
      "page": "c_net_annotate",
      "title": "Annotate a metanet",
      "concept": [
        "manipulate"
      ],
      "topics": [
        "c_net_annotate"
      ]
    },
    {
      "page": "c_net_build",
      "title": "Construct a metanet from a corr object",
      "concept": [
        "build"
      ],
      "topics": [
        "c_net_build"
      ]
    },
    {
      "page": "c_net_calculate",
      "title": "Calculate correlation for one or two t(otutab), or distance for one t(otutab).",
      "concept": [
        "calculate"
      ],
      "topics": [
        "c_net_cal",
        "c_net_calculate"
      ]
    },
    {
      "page": "c_net_compare",
      "title": "Compare Two Networks",
      "topics": [
        "c_net_compare"
      ]
    },
    {
      "page": "c_net_difference",
      "title": "Difference two networks",
      "topics": [
        "c_net_difference"
      ]
    },
    {
      "page": "c_net_ego",
      "title": "Extract ego-centric subnetwork with preserved class attributes",
      "topics": [
        "c_net_ego",
        "c_net_neighbors"
      ]
    },
    {
      "page": "c_net_filter",
      "title": "Filter a network according to some attributes",
      "concept": [
        "manipulate"
      ],
      "topics": [
        "c_net_filter"
      ]
    },
    {
      "page": "c_net_from_edgelist",
      "title": "Construct a network from edge_list dataframe",
      "concept": [
        "build"
      ],
      "topics": [
        "c_net_from_edgelist"
      ]
    },
    {
      "page": "c_net_highlight",
      "title": "Highlight specific nodes in a network",
      "topics": [
        "c_net_highlight"
      ]
    },
    {
      "page": "c_net_intersect",
      "title": "Intersect two networks",
      "topics": [
        "c_net_intersect"
      ]
    },
    {
      "page": "c_net_layout",
      "title": "Layout coordinates",
      "concept": [
        "layout"
      ],
      "topics": [
        "c_net_lay",
        "c_net_layout"
      ]
    },
    {
      "page": "c_net_load",
      "title": "Load network file",
      "concept": [
        "manipulate"
      ],
      "topics": [
        "c_net_load"
      ]
    },
    {
      "page": "c_net_plot",
      "title": "Plot a metanet",
      "concept": [
        "plot"
      ],
      "topics": [
        "c_net_plot"
      ]
    },
    {
      "page": "c_net_save",
      "title": "Save network file",
      "concept": [
        "manipulate"
      ],
      "topics": [
        "c_net_save"
      ]
    },
    {
      "page": "c_net_set",
      "title": "Set basic attributes from totu table",
      "concept": [
        "build"
      ],
      "topics": [
        "c_net_set"
      ]
    },
    {
      "page": "c_net_stability",
      "title": "Evaluate the stability of a network",
      "topics": [
        "c_net_stability",
        "robustness",
        "robust_test",
        "vulnerability"
      ]
    },
    {
      "page": "c_net_union",
      "title": "Union two networks",
      "concept": [
        "manipulate"
      ],
      "topics": [
        "c_net_union"
      ]
    },
    {
      "page": "c_net_update",
      "title": "Update a metanet object or transform igraph object to metanet object",
      "concept": [
        "build"
      ],
      "topics": [
        "as.metanet",
        "c_net_update"
      ]
    },
    {
      "page": "cal_sim",
      "title": "Calculate similarity for one t(otutab)",
      "concept": [
        "calculate"
      ],
      "topics": [
        "cal_sim"
      ]
    },
    {
      "page": "check_tabs",
      "title": "Check tables and extract common samples",
      "topics": [
        "check_tabs"
      ]
    },
    {
      "page": "clean_igraph",
      "title": "Clean a igraph object",
      "topics": [
        "clean_igraph"
      ]
    },
    {
      "page": "clean_multi_edge_metanet",
      "title": "Clean multi edge metanet to plot",
      "topics": [
        "clean_multi_edge_metanet"
      ]
    },
    {
      "page": "co_net",
      "title": "MetaNet networks",
      "topics": [
        "co_net"
      ]
    },
    {
      "page": "co_net_rmt",
      "title": "MetaNet networks",
      "topics": [
        "co_net_rmt"
      ]
    },
    {
      "page": "co_net2",
      "title": "MetaNet networks",
      "topics": [
        "co_net2"
      ]
    },
    {
      "page": "Cohesion",
      "title": "Cohesion calculation",
      "topics": [
        "Cohesion",
        "plot.cohesion"
      ]
    },
    {
      "page": "df2net_tree",
      "title": "Transform a dataframe to a network edgelist.",
      "topics": [
        "df2net_tree"
      ]
    },
    {
      "page": "extract_sample_net",
      "title": "Extract each sample network from the whole network",
      "concept": [
        "topological"
      ],
      "topics": [
        "extract_sample_net"
      ]
    },
    {
      "page": "fast_cor",
      "title": "Fast correlation calculation",
      "concept": [
        "calculate"
      ],
      "topics": [
        "fast_cor"
      ]
    },
    {
      "page": "filter_n_module",
      "title": "Filter some modules as others",
      "concept": [
        "module"
      ],
      "topics": [
        "combine_n_module",
        "filter_n_module",
        "plot_module_tree"
      ]
    },
    {
      "page": "fit_power",
      "title": "Fit power-law distribution for an igraph",
      "concept": [
        "topological"
      ],
      "topics": [
        "fit_power"
      ]
    },
    {
      "page": "g_layout",
      "title": "Layout with group",
      "concept": [
        "g_layout"
      ],
      "topics": [
        "g_layout"
      ]
    },
    {
      "page": "g_layout_nice",
      "title": "Layout with group nicely",
      "concept": [
        "g_layout"
      ],
      "topics": [
        "get_big_lay_nice",
        "g_layout_backbone",
        "g_layout_circlepack",
        "g_layout_nice",
        "g_layout_stress",
        "g_layout_treemap"
      ]
    },
    {
      "page": "g_layout_poly_sector",
      "title": "Layout with group",
      "concept": [
        "g_layout"
      ],
      "topics": [
        "g_layout_poly_sector"
      ]
    },
    {
      "page": "g_layout_polygon",
      "title": "Layout with group as a polygon",
      "concept": [
        "g_layout"
      ],
      "topics": [
        "g_layout_multi_layer",
        "g_layout_polyarc",
        "g_layout_polycircle",
        "g_layout_polygon"
      ]
    },
    {
      "page": "get_community",
      "title": "Get community",
      "concept": [
        "module"
      ],
      "topics": [
        "get_community"
      ]
    },
    {
      "page": "get_e",
      "title": "Get edge information",
      "concept": [
        "manipulate"
      ],
      "topics": [
        "get_e"
      ]
    },
    {
      "page": "get_group_skeleton",
      "title": "Get skeleton network according to a group",
      "concept": [
        "topological"
      ],
      "topics": [
        "c_net_skeleton",
        "get_group_skeleton",
        "skeleton_plot"
      ]
    },
    {
      "page": "get_module",
      "title": "Get module",
      "concept": [
        "module"
      ],
      "topics": [
        "get_module"
      ]
    },
    {
      "page": "get_module_eigen",
      "title": "Get module_eigen",
      "concept": [
        "module"
      ],
      "topics": [
        "get_module_eigen"
      ]
    },
    {
      "page": "get_n",
      "title": "Get network information",
      "concept": [
        "manipulate"
      ],
      "topics": [
        "get_n"
      ]
    },
    {
      "page": "get_v",
      "title": "Get vertex information",
      "concept": [
        "manipulate"
      ],
      "topics": [
        "get_v"
      ]
    },
    {
      "page": "input_cytoscape",
      "title": "Input a cyjs file exported by Cytoscape",
      "concept": [
        "plot"
      ],
      "topics": [
        "input_cytoscape"
      ]
    },
    {
      "page": "input_gephi",
      "title": "Input a graphml file exported by Gephi",
      "concept": [
        "plot"
      ],
      "topics": [
        "input_gephi"
      ]
    },
    {
      "page": "is_metanet",
      "title": "Is this object a metanet object?",
      "concept": [
        "manipulate"
      ],
      "topics": [
        "is.metanet",
        "is_metanet"
      ]
    },
    {
      "page": "links_stat",
      "title": "Link summary of the network",
      "concept": [
        "topological"
      ],
      "topics": [
        "links_stat"
      ]
    },
    {
      "page": "metab",
      "title": "MetaNet networks abundance",
      "topics": [
        "metab"
      ]
    },
    {
      "page": "metab_g",
      "title": "MetaNet networks metadata",
      "topics": [
        "metab_g"
      ]
    },
    {
      "page": "micro",
      "title": "MetaNet networks abundance",
      "topics": [
        "micro"
      ]
    },
    {
      "page": "micro_g",
      "title": "MetaNet networks metadata",
      "topics": [
        "micro_g"
      ]
    },
    {
      "page": "module_detect",
      "title": "Detect the modules",
      "concept": [
        "module"
      ],
      "topics": [
        "c_net_module",
        "module_detect"
      ]
    },
    {
      "page": "module_expression",
      "title": "Calculate the eigenvalue of each module and correlation of nodes and eigenvalue (node_eigen_cor).",
      "concept": [
        "module"
      ],
      "topics": [
        "module_eigen",
        "module_expression"
      ]
    },
    {
      "page": "module_net",
      "title": "Generate a n-modules network",
      "concept": [
        "module"
      ],
      "topics": [
        "module_net"
      ]
    },
    {
      "page": "multi_net_build",
      "title": "Multi-omics network build",
      "concept": [
        "build"
      ],
      "topics": [
        "multi_net_build"
      ]
    },
    {
      "page": "multi1",
      "title": "MetaNet networks",
      "topics": [
        "multi1"
      ]
    },
    {
      "page": "nc",
      "title": "Calculate natural_connectivity",
      "concept": [
        "topological"
      ],
      "topics": [
        "nc"
      ]
    },
    {
      "page": "net_par",
      "title": "Calculate all topological indexes of a network",
      "concept": [
        "topological"
      ],
      "topics": [
        "c_net_index",
        "net_par"
      ]
    },
    {
      "page": "netD3plot",
      "title": "plot use networkD3",
      "concept": [
        "plot"
      ],
      "topics": [
        "netD3plot"
      ]
    },
    {
      "page": "olympic_rings_net",
      "title": "Plot olympic rings using network",
      "concept": [
        "plot"
      ],
      "topics": [
        "olympic_rings_net"
      ]
    },
    {
      "page": "p.adjust.table",
      "title": "p.adjust apply on a correlation table (matrix or data.frame)",
      "concept": [
        "calculate"
      ],
      "topics": [
        "p.adjust.table"
      ]
    },
    {
      "page": "plot_corr_heatmap",
      "title": "Plot a correlation heatmap",
      "topics": [
        "plot_corr_heatmap"
      ]
    },
    {
      "page": "plot_e_type_bar",
      "title": "Plot e_type bar",
      "topics": [
        "plot_e_type_bar"
      ]
    },
    {
      "page": "plot_multi_nets",
      "title": "Batch drawing multiple network diagrams",
      "topics": [
        "plot_multi_nets"
      ]
    },
    {
      "page": "plot_net_degree",
      "title": "Plot degree distribution of networks",
      "topics": [
        "plot_net_degree"
      ]
    },
    {
      "page": "plot.ggig",
      "title": "Plot a ggig",
      "concept": [
        "plot"
      ],
      "topics": [
        "plot.ggig"
      ]
    },
    {
      "page": "plot.metanet",
      "title": "Plot a metanet",
      "topics": [
        "plot.metanet"
      ]
    },
    {
      "page": "plot.metanet_compare",
      "title": "Plot a metanet_compare",
      "topics": [
        "plot.metanet_compare"
      ]
    },
    {
      "page": "plot.rmt_res",
      "title": "Plot a rmt_res",
      "topics": [
        "plot.rmt_res"
      ]
    },
    {
      "page": "robust_test",
      "title": "Plot robust",
      "topics": [
        "plot.robust"
      ]
    },
    {
      "page": "robustness",
      "title": "Plot robustness",
      "topics": [
        "plot.robustness"
      ]
    },
    {
      "page": "vulnerability",
      "title": "Plot vulnerability",
      "topics": [
        "plot.vulnerability"
      ]
    },
    {
      "page": "print.cohesion",
      "title": "Print method for 'cohesion' objects",
      "topics": [
        "print.cohesion"
      ]
    },
    {
      "page": "print.coors",
      "title": "Print method for 'coors' objects",
      "topics": [
        "print.coors"
      ]
    },
    {
      "page": "print.corr",
      "title": "Print method for 'corr' objects",
      "topics": [
        "print.corr"
      ]
    },
    {
      "page": "print.ggig",
      "title": "Print method for 'ggig' objects",
      "topics": [
        "print.ggig"
      ]
    },
    {
      "page": "print.metanet",
      "title": "Print method for 'metanet' objects",
      "topics": [
        "print.metanet"
      ]
    },
    {
      "page": "print.metanet_compare",
      "title": "Print method for 'metanet_compare' objects",
      "topics": [
        "print.metanet_compare"
      ]
    },
    {
      "page": "print.robust",
      "title": "Print method for 'robust' objects",
      "topics": [
        "print.robust"
      ]
    },
    {
      "page": "print.robustness",
      "title": "Print method for 'robustness' objects",
      "topics": [
        "print.robustness"
      ]
    },
    {
      "page": "print.vulnerability",
      "title": "Print method for 'vulnerability' objects",
      "topics": [
        "print.vulnerability"
      ]
    },
    {
      "page": "rand_net",
      "title": "Degree distribution comparison with random network",
      "concept": [
        "topological"
      ],
      "topics": [
        "rand_net"
      ]
    },
    {
      "page": "compare_rand",
      "title": "Net_pars of many random network",
      "concept": [
        "topological"
      ],
      "topics": [
        "compare_rand",
        "rand_net_par"
      ]
    },
    {
      "page": "read_corr",
      "title": "Read a corr object",
      "concept": [
        "calculate"
      ],
      "topics": [
        "read_corr"
      ]
    },
    {
      "page": "RMT_threshold",
      "title": "Get RMT threshold for a correlation matrix",
      "topics": [
        "rmt",
        "RMT_threshold"
      ]
    },
    {
      "page": "save_corr",
      "title": "Save a corr object",
      "topics": [
        "save_corr"
      ]
    },
    {
      "page": "show_MetaNet_logo",
      "title": "Show MetaNet logo",
      "topics": [
        "show_MetaNet_logo"
      ]
    },
    {
      "page": "smallworldness",
      "title": "Calculate small-world coefficient",
      "concept": [
        "topological"
      ],
      "topics": [
        "smallworldness"
      ]
    },
    {
      "page": "spatstat_layout",
      "title": "Generate spatial layout using 'spatstat'",
      "topics": [
        "spatstat_layout"
      ]
    },
    {
      "page": "summ_2col",
      "title": "Summaries two columns information",
      "topics": [
        "summ_2col"
      ]
    },
    {
      "page": "summary_module",
      "title": "Summary module index",
      "concept": [
        "module"
      ],
      "topics": [
        "summary_module"
      ]
    },
    {
      "page": "summary.corr",
      "title": "Summary method for 'corr' objects",
      "topics": [
        "summary.corr"
      ]
    },
    {
      "page": "to_module_net",
      "title": "Transformation a network to a module network",
      "concept": [
        "module"
      ],
      "topics": [
        "to_module_net"
      ]
    },
    {
      "page": "transc",
      "title": "MetaNet networks abundance",
      "topics": [
        "transc"
      ]
    },
    {
      "page": "transc_g",
      "title": "MetaNet networks metadata",
      "topics": [
        "transc_g"
      ]
    },
    {
      "page": "transform_coors",
      "title": "Transform the layout of a 'coors' object",
      "topics": [
        "transform_coors"
      ]
    },
    {
      "page": "twocol_edgelist",
      "title": "Quick build a metanet from two columns table",
      "concept": [
        "plot"
      ],
      "topics": [
        "twocol_edgelist"
      ]
    },
    {
      "page": "venn_net",
      "title": "Venn network",
      "concept": [
        "plot"
      ],
      "topics": [
        "venn_net"
      ]
    },
    {
      "page": "zp_analyse",
      "title": "Zi-Pi calculate",
      "concept": [
        "module"
      ],
      "topics": [
        "zp_analyse",
        "zp_plot"
      ]
    }
  ],
  "_pkglogo": "https://github.com/asa12138/metanet/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/asa12138/metanet/raw/HEAD/README.md",
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  "_vignettes": [
    {
      "source": "MetaNet.Rmd",
      "filename": "MetaNet.html",
      "title": "MetaNet: Network Analysis for Omics Data",
      "author": "Chen Peng",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Install",
        "Vignette",
        "Citation",
        "Need helps?"
      ],
      "created": "2023-06-25 04:39:39",
      "modified": "2024-03-21 08:01:19",
      "commits": 5
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  "_score": 7.425534220498264,
  "_indexed": true,
  "_nocasepkg": "metanet",
  "_universes": [
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