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  "Package": "SeqNet",
  "Title": "Generate RNA-Seq Data from Gene-Gene Association Networks",
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  "Authors@R": "c(person(\"Tyler\", \"Grimes\", role = c(\"aut\", \"cre\"),\nemail = \"tyler.grimes@unf.edu\"),\nperson(\"Somnath\", \"Datta\", role = c(\"aut\")))",
  "Author": "Tyler Grimes [aut, cre], Somnath Datta [aut]",
  "Maintainer": "Tyler Grimes <tyler.grimes@unf.edu>",
  "Description": "Methods to generate random gene-gene association networks\nand simulate RNA-seq data from them, as described in Grimes and\nDatta (2021) <doi:10.18637/jss.v098.i12>. Includes functions to\ngenerate random networks of any size and perturb them to obtain\ndifferential networks. Network objects are built from\nindividual, overlapping modules that represent pathways. The\nresulting network has various topological properties that are\ncharacteristic of gene regulatory networks. RNA-seq data can be\ngenerated such that the association among gene expression\nprofiles reflect the underlying network. A reference RNA-seq\ndataset can be provided to model realistic marginal\ndistributions. Plotting functions are available to visualize a\nnetwork, compare two networks, and compare the expression of\ntwo genes across multiple networks.",
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  "Date/Publication": "2026-10-10 13:52:06 UTC",
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    "author": "Tyler Grimes <tyler.grimes@unf.edu>",
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    "as_single_module",
    "check_adjacency_cpp",
    "components_in_adjacency",
    "connect_module_structure",
    "create_cytoscape_file",
    "create_empty_module",
    "create_empty_network",
    "create_module_from_adjacency_matrix",
    "create_module_from_association_matrix",
    "create_modules_for_network",
    "create_network_from_adjacency_matrix",
    "create_network_from_association_matrix",
    "create_network_from_modules",
    "dzinb",
    "ecdf_cpp",
    "edges_from_adjacency_cpp",
    "est_params_from_reference",
    "gen_gaussian",
    "gen_partial_correlations",
    "gen_rnaseq",
    "gen_zinb",
    "get_adjacency_matrix",
    "get_association_matrix",
    "get_degree_distribution",
    "get_edge_weights_from_module",
    "get_network_characteristics",
    "get_network_modules",
    "get_node_names",
    "get_sigma",
    "get_summary_for_node",
    "heatmap_network",
    "is_symmetric_cpp",
    "is_weighted",
    "perturb_network",
    "plot_gene_pair",
    "plot_modules",
    "plot_network",
    "plot_network_diff",
    "plot_network_sim",
    "pzinb",
    "qzinb",
    "random_module",
    "random_module_structure",
    "random_network",
    "remove_connections",
    "remove_connections_to_node",
    "remove_weights",
    "rewire_connections",
    "rewire_connections_to_node",
    "ring_lattice_cpp",
    "rzinb",
    "sample_link_nodes",
    "sample_module_nodes",
    "sample_reference_data",
    "set_module_name",
    "set_node_names",
    "update_module_with_random_weights"
  ],
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      "name": "reference",
      "title": "RNA-seq reference dataset",
      "object": "reference",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add_modules_to_network",
      "title": "Internal function for adding a set of modules to the network",
      "topics": [
        "add_modules_to_network"
      ]
    },
    {
      "page": "add_random_module_to_network",
      "title": "Adds a random module of a given size to the network",
      "topics": [
        "add_random_module_to_network"
      ]
    },
    {
      "page": "as_single_module",
      "title": "Collapses all modules in network into a single module",
      "topics": [
        "as_single_module"
      ]
    },
    {
      "page": "check_adjacency_cpp",
      "title": "C++ implementation to check if a matrix is an adjacency matrix",
      "topics": [
        "check_adjacency_cpp"
      ]
    },
    {
      "page": "components_in_adjacency",
      "title": "C++ implementation to obtain connected components in a graph.",
      "topics": [
        "components_in_adjacency"
      ]
    },
    {
      "page": "connect_module_structure",
      "title": "Connect disconnected components in an adjacency matrix",
      "topics": [
        "connect_module_structure"
      ]
    },
    {
      "page": "create_cytoscape_file",
      "title": "Create an edge table file for Cytoscape",
      "topics": [
        "create_cytoscape_file"
      ]
    },
    {
      "page": "create_empty_module",
      "title": "Create a module",
      "topics": [
        "create_empty_module"
      ]
    },
    {
      "page": "create_empty_network",
      "title": "Create a network object.",
      "topics": [
        "create_empty_network"
      ]
    },
    {
      "page": "create_module_from_adjacency_matrix",
      "title": "Create a module from an adjacency matrix",
      "topics": [
        "create_module_from_adjacency_matrix"
      ]
    },
    {
      "page": "create_module_from_association_matrix",
      "title": "Create a module from an association matrix",
      "topics": [
        "create_module_from_association_matrix"
      ]
    },
    {
      "page": "create_modules_for_network",
      "title": "Randomly sample subsets of genes for each module",
      "topics": [
        "create_modules_for_network"
      ]
    },
    {
      "page": "create_network_from_adjacency_matrix",
      "title": "Create a network object from an adjacency matrix",
      "topics": [
        "create_network_from_adjacency_matrix"
      ]
    },
    {
      "page": "create_network_from_association_matrix",
      "title": "Create a network object from an association matrix",
      "topics": [
        "create_network_from_association_matrix"
      ]
    },
    {
      "page": "create_network_from_modules",
      "title": "Create a network object.",
      "topics": [
        "create_network_from_modules"
      ]
    },
    {
      "page": "dzinb",
      "title": "The Zero-Inflated Negative Binomial Distribution",
      "topics": [
        "dzinb"
      ]
    },
    {
      "page": "ecdf_cpp",
      "title": "C++ implementation of empirical CDF",
      "topics": [
        "ecdf_cpp"
      ]
    },
    {
      "page": "edges_from_adjacency_cpp",
      "title": "C++ implementation for obtaining an edge list from adjacency matrix",
      "topics": [
        "edges_from_adjacency_cpp"
      ]
    },
    {
      "page": "est_params_from_reference",
      "title": "Estimate ZINB parameters from reference data",
      "topics": [
        "est_params_from_reference"
      ]
    },
    {
      "page": "gen_gaussian",
      "title": "Generate observations from a Gaussian graphical model.",
      "topics": [
        "gen_gaussian"
      ]
    },
    {
      "page": "gen_partial_correlations",
      "title": "Generate partial correlations for a list of networks.",
      "topics": [
        "gen_partial_correlations"
      ]
    },
    {
      "page": "gen_rnaseq",
      "title": "Generate RNA-seq data from an underlying network",
      "topics": [
        "gen_rnaseq"
      ]
    },
    {
      "page": "gen_zinb",
      "title": "Generate ZINB counts from an underlying network",
      "topics": [
        "gen_zinb"
      ]
    },
    {
      "page": "get_adjacency_matrix",
      "title": "Get adjacency matrix",
      "topics": [
        "get_adjacency_matrix"
      ]
    },
    {
      "page": "get_adjacency_matrix.default",
      "title": "Get adjacency matrix",
      "topics": [
        "get_adjacency_matrix.default"
      ]
    },
    {
      "page": "get_adjacency_matrix.matrix",
      "title": "Get adjacency matrix",
      "topics": [
        "get_adjacency_matrix.matrix"
      ]
    },
    {
      "page": "get_adjacency_matrix.network",
      "title": "Get adjacency matrix",
      "topics": [
        "get_adjacency_matrix.network"
      ]
    },
    {
      "page": "get_adjacency_matrix.network_module",
      "title": "Get adjacency matrix",
      "topics": [
        "get_adjacency_matrix.network_module"
      ]
    },
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      "page": "get_association_matrix",
      "title": "Get association matrix",
      "topics": [
        "get_association_matrix"
      ]
    },
    {
      "page": "get_association_matrix.default",
      "title": "Get association matrix",
      "topics": [
        "get_association_matrix.default"
      ]
    },
    {
      "page": "get_association_matrix.matrix",
      "title": "Get association matrix",
      "topics": [
        "get_association_matrix.matrix"
      ]
    },
    {
      "page": "get_association_matrix.network",
      "title": "Get association matrix",
      "topics": [
        "get_association_matrix.network"
      ]
    },
    {
      "page": "get_association_matrix.network_module",
      "title": "Get association matrix",
      "topics": [
        "get_association_matrix.network_module"
      ]
    },
    {
      "page": "get_degree_distribution",
      "title": "Get the degree distribution for a network.",
      "topics": [
        "get_degree_distribution"
      ]
    },
    {
      "page": "get_edge_weights_from_module",
      "title": "Get edge weights.",
      "topics": [
        "get_edge_weights_from_module"
      ]
    },
    {
      "page": "get_layout_for_modules",
      "title": "Internal function used to create coordinates based on a set of modules",
      "topics": [
        "get_layout_for_modules"
      ]
    },
    {
      "page": "get_network_characteristics",
      "title": "Characteristics of the network topology",
      "topics": [
        "get_network_characteristics"
      ]
    },
    {
      "page": "get_network_modules",
      "title": "Get a list of modules from the network",
      "topics": [
        "get_network_modules"
      ]
    },
    {
      "page": "get_node_names",
      "title": "Get node names",
      "topics": [
        "get_node_names"
      ]
    },
    {
      "page": "get_node_names.default",
      "title": "Get node names",
      "topics": [
        "get_node_names.default"
      ]
    },
    {
      "page": "get_node_names.matrix",
      "title": "Get node names",
      "topics": [
        "get_node_names.matrix"
      ]
    },
    {
      "page": "get_node_names.network",
      "title": "Get node names",
      "topics": [
        "get_node_names.network"
      ]
    },
    {
      "page": "get_node_names.network_module",
      "title": "Get node names",
      "topics": [
        "get_node_names.network_module"
      ]
    },
    {
      "page": "get_sigma",
      "title": "Get the covariance matrix",
      "topics": [
        "get_sigma"
      ]
    },
    {
      "page": "get_sigma.default",
      "title": "Get the covariance matrix",
      "topics": [
        "get_sigma.default"
      ]
    },
    {
      "page": "get_sigma.matrix",
      "title": "Get the covariance matrix",
      "topics": [
        "get_sigma.matrix"
      ]
    },
    {
      "page": "get_sigma.network",
      "title": "Get the covariance matrix",
      "topics": [
        "get_sigma.network"
      ]
    },
    {
      "page": "get_sigma.network_module",
      "title": "Get the covariance matrix",
      "topics": [
        "get_sigma.network_module"
      ]
    },
    {
      "page": "get_summary_for_node",
      "title": "Get summary for a node in the network.",
      "topics": [
        "get_summary_for_node"
      ]
    },
    {
      "page": "heatmap_network",
      "title": "Plot heatmap representation of a network",
      "topics": [
        "heatmap_network"
      ]
    },
    {
      "page": "is_symmetric_cpp",
      "title": "C++ implementation to check if a matrix is symmetric",
      "topics": [
        "is_symmetric_cpp"
      ]
    },
    {
      "page": "is_weighted",
      "title": "Check if an object is weighted",
      "topics": [
        "is_weighted"
      ]
    },
    {
      "page": "is_weighted.default",
      "title": "Check if an object is weighted",
      "topics": [
        "is_weighted.default"
      ]
    },
    {
      "page": "is_weighted.matrix",
      "title": "Check if an object is weighted",
      "topics": [
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      ]
    },
    {
      "page": "is_weighted.network",
      "title": "Check if an object is weighted",
      "topics": [
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    },
    {
      "page": "is_weighted.network_module",
      "title": "Check if an object is weighted",
      "topics": [
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    },
    {
      "page": "perturb_network",
      "title": "Perturbs the connections in a network",
      "topics": [
        "perturb_network"
      ]
    },
    {
      "page": "plot_gene_pair",
      "title": "Scatter plot of two gene expressions",
      "topics": [
        "plot_gene_pair"
      ]
    },
    {
      "page": "plot_modules",
      "title": "Visualize a network and its modules",
      "topics": [
        "plot_modules"
      ]
    },
    {
      "page": "plot_network",
      "title": "Visualize a network",
      "topics": [
        "plot_network"
      ]
    },
    {
      "page": "plot_network_diff",
      "title": "Plot the difference between two networks",
      "topics": [
        "plot_network_diff"
      ]
    },
    {
      "page": "plot_network_sim",
      "title": "Plot the similarity between two networks",
      "topics": [
        "plot_network_sim"
      ]
    },
    {
      "page": "plot.network",
      "title": "Plot function for 'network' object",
      "topics": [
        "plot.network"
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    },
    {
      "page": "plot.network_module",
      "title": "Plot function for 'network_module' object.",
      "topics": [
        "plot.network_module"
      ]
    },
    {
      "page": "plot.network_plot",
      "title": "Plot function for 'network_plot' class",
      "topics": [
        "plot.network_plot"
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    },
    {
      "page": "print.network",
      "title": "Print function for 'network' object.",
      "topics": [
        "print.network"
      ]
    },
    {
      "page": "print.network_module",
      "title": "Print function for 'network_module' object.",
      "topics": [
        "print.network_module"
      ]
    },
    {
      "page": "print.network_plot",
      "title": "Print function for 'network_plot' class",
      "topics": [
        "print.network_plot"
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    {
      "page": "pzinb",
      "title": "The Zero-Inflated Negative Binomial Distribution",
      "topics": [
        "pzinb"
      ]
    },
    {
      "page": "qzinb",
      "title": "The Zero-Inflated Negative Binomial Distribution",
      "topics": [
        "qzinb"
      ]
    },
    {
      "page": "random_module",
      "title": "Create a random module",
      "topics": [
        "random_module"
      ]
    },
    {
      "page": "random_module_structure",
      "title": "Create a random network structure for a module",
      "topics": [
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    },
    {
      "page": "random_network",
      "title": "Create a network object.",
      "topics": [
        "random_network"
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    },
    {
      "page": "reference",
      "title": "RNA-seq reference dataset",
      "topics": [
        "reference"
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    },
    {
      "page": "remove_connections",
      "title": "Remove connections in a network",
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