{ "_id": "6acb6c52fe5cc25786e8fd3b", "Package": "SeqNet", "Title": "Generate RNA-Seq Data from Gene-Gene Association Networks", "Version": "1.1.4", "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 ", "Description": "Methods to generate random gene-gene association networks\nand simulate RNA-seq data from them, as described in Grimes and\nDatta (2021) . 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.", "RdMacros": "Rdpack", "VignetteBuilder": "knitr", "License": "GPL-2 | GPL-3", "Encoding": "UTF-8", "LazyData": "true", "LazyDataCompression": "xz", "RoxygenNote": "7.1.1", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://tgrimes.r-universe.dev", "Date/Publication": "2026-09-28 21:55:24 UTC", "RemoteUrl": "https://github.com/tgrimes/seqnet", "RemoteRef": "HEAD", "RemoteSha": "bf4e8b07862c1376ccf93ab5ae445816228a45ef", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-11 10:49:51 UTC", "User": "root" }, "_user": "tgrimes", "_type": "src", "_file": "SeqNet_1.1.4.tar.gz", "_fileid": "https://r2.ropensci.org/07c9b068cfb71d7563479ef9bbbcd8bc5225a40daac3a927de6e77fd980a1fd3", "_filesize": 1933958, "_sha256": "07c9b068cfb71d7563479ef9bbbcd8bc5225a40daac3a927de6e77fd980a1fd3", "_expires": "2027-01-19T11:00:32.000Z", "_created": "2026-10-11T10:49:51.000Z", "_published": "2026-10-11T11:00:34.488Z", "_buildurl": "https://github.com/r-universe/tgrimes/actions/runs/38133118296", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 114452164385, "time": 149, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11699724107" }, { "job": 114452164400, "time": 128, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11699544311" }, { "job": 114452164434, "time": 142, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11699709110" }, { "job": 114452164494, "time": 140, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11700176502" }, { "job": 114452164454, "time": 219, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11699519910" }, { "job": 114452164443, "time": 301, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11700017398" }, { "job": 114452164399, "time": 163, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11699634662" }, { "job": 114452164394, "time": 373, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11700141858" }, { "job": 114451418420, "time": 252, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11700031674" }, { "job": 114452164326, "time": 111, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11700221364" }, { "job": 114452164421, "time": 380, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11700311631" }, { "job": 114452164456, "time": 148, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11699289833" }, { "job": 114452164483, "time": 134, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11699444507" }, { "job": 114452164444, "time": 354, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11699644611" }, { "job": 114452164474, "time": 145, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11699848721" } ], "_upstream": "https://github.com/tgrimes/seqnet", "_commit": { "id": "bf4e8b07862c1376ccf93ab5ae445816228a45ef", "author": "t-grimes ", "committer": "t-grimes ", "message": "Shrink bundled reference dataset; add introductory vignette\n\ndata/reference.rda reduced from 1.1.3's 516x6022 (4.88 MB) to a\n200x2000 random subsample (0.66 MB, seed 20260928), keeping all\n6022->2000 genes' worth of marginal-distribution diversity that\nsample_reference_data() draws on while cutting the installed package\nsize well below where CRAN's size check tends to fire (confirmed:\n\"checking installed package size\" goes from an INFO to a clean OK).\nVerified the new sample size doesn't distort the empirical marginals\nthat gen_rnaseq()'s inverse-transform sampling relies on (checked\nmean/proportion-zero/90th-percentile across several genes, full vs.\nsubsampled).\n\nR/data.R and man/reference.Rd previously documented dimensions\n(1093 x 15944) that didn't even match the actual bundled data\n(516 x 6022) -- and called it a \"data frame\" when it's a matrix.\nFixed both regardless of the resize.\n\nplot_gene_pair()'s example indexed reference rows 201:250, which no\nlonger exist at 200 rows; rescaled to 1:50/51:100/101:150.\n\nAdded vignettes/SeqNet.Rmd, a walkthrough of the core workflow\n(network creation, modules, edge weights, gen_rnaseq vs. gen_zinb,\ndifferential networks via perturb_network, plot_gene_pair) -- which\nalso means the knitr/rmarkdown Suggests entries are now actually\nused. Added VignetteBuilder: knitr to DESCRIPTION.\n\nVerified R CMD check --as-cran on the full built package (vignette\nincluded) returns a single NOTE -- CRAN's automatic \"previously\narchived\" notice, not a defect -- with all other checks OK, including\nre-building of vignette outputs.\n\nCo-Authored-By: Claude Sonnet 5 \n", "time": 1790632524 }, "_maintainer": { "name": "Tyler Grimes", "email": "tyler.grimes@unf.edu", "login": "tgrimes", "description": "Personal website:", "uuid": 16945884 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "fitdistrplus", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": 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] }, { "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" ] }, { "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": [ "is_weighted.matrix" ] }, { "page": "is_weighted.network", "title": "Check if an object is weighted", "topics": [ "is_weighted.network" ] }, { "page": "is_weighted.network_module", "title": "Check if an object is weighted", "topics": [ "is_weighted.network_module" ] }, { "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" ] }, { "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" ] }, { "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" ] }, { "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": [ "random_module_structure" ] }, { "page": "random_network", "title": "Create a network object.", "topics": [ "random_network" ] }, { "page": "reference", "title": "RNA-seq reference dataset", "topics": [ "reference" ] }, { "page": "remove_connections", "title": "Remove connections in a network", "topics": [ "remove_connections" ] }, { "page": "remove_connections_to_node", "title": "Remove connections to a node", "topics": [ "remove_connections_to_node" ] }, { "page": "remove_connections_to_node.default", "title": "Remove connections to a node", "topics": [ "remove_connections_to_node.default" ] }, { "page": "remove_connections_to_node.matrix", "title": "Remove connections to a node", "topics": [ "remove_connections_to_node.matrix" ] }, { "page": "remove_connections_to_node.network", "title": "Remove connections to a node", "topics": [ "remove_connections_to_node.network" ] }, { "page": "remove_connections_to_node.network_module", "title": "Remove connections to a node", "topics": [ "remove_connections_to_node.network_module" ] }, { "page": "remove_connections.default", "title": "Remove connections in a network", "topics": [ "remove_connections.default" ] }, { "page": "remove_connections.matrix", "title": "Remove connections in a network", "topics": [ "remove_connections.matrix" ] }, { "page": "remove_connections.network", "title": "Remove connections in a network", "topics": [ "remove_connections.network" ] }, { "page": "remove_connections.network_module", "title": "Remove connections in a network", "topics": [ "remove_connections.network_module" ] }, { "page": "remove_weights", "title": "Removes the weights of all connections", "topics": [ "remove_weights" ] }, { "page": "remove_weights.default", "title": "Removes the weights of all connections", "topics": [ "remove_weights.default" ] }, { "page": "remove_weights.matrix", "title": "Removes the weights of all connections", "topics": [ "remove_weights.matrix" ] }, { "page": "remove_weights.network", "title": "Removes the weights of all connections", "topics": [ "remove_weights.network" ] }, { "page": "remove_weights.network_module", "title": "Removes the weights of all connections", "topics": [ "remove_weights.network_module" ] }, { "page": "replace_module_in_network", "title": "Internal function for replacing a module in the network", "topics": [ "replace_module_in_network" ] }, { "page": "rewire_connections", "title": "Rewire connections", "topics": [ "rewire_connections" ] }, { "page": "rewire_connections_to_node", "title": "Rewire connections to a node", "topics": [ "rewire_connections_to_node" ] }, { "page": "rewire_connections_to_node.default", "title": "Rewire connections to a node", "topics": [ "rewire_connections_to_node.default" ] }, { "page": "rewire_connections_to_node.matrix", "title": "Rewire connections to a node", "topics": [ "rewire_connections_to_node.matrix" ] }, { "page": "rewire_connections_to_node.network", "title": "Rewire connections to a node", "topics": [ "rewire_connections_to_node.network" ] }, { "page": "rewire_connections_to_node.network_module", "title": "Rewire connections to a node", "topics": [ "rewire_connections_to_node.network_module" ] }, { "page": "rewire_connections.default", "title": "Rewire connections", "topics": [ "rewire_connections.default" ] }, { "page": "rewire_connections.matrix", "title": "Rewire connections", "topics": [ "rewire_connections.matrix" ] }, { "page": "rewire_connections.network", "title": "Rewire connections", "topics": [ "rewire_connections.network" ] }, { "page": "rewire_connections.network_module", "title": "Rewire connections", "topics": [ "rewire_connections.network_module" ] }, { "page": "ring_lattice_cpp", "title": "C++ implementation for creating a ring lattice", "topics": [ "ring_lattice_cpp" ] }, { "page": "rzinb", "title": "The Zero-Inflated Negative Binomial Distribution", "topics": [ "rzinb" ] }, { "page": "sample_link_nodes", "title": "Sample link 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