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SeqNet
View on CRAN: Click
here
Download and install SeqNet package within the R console
Install from CRAN:
install.packages("SeqNet")
Install from Github:
library("remotes")
install_github("cran/SeqNet")
Install by package version:
library("remotes")
install_version("SeqNet", "1.1.3")
Attach the package and use:
library("SeqNet")
Maintained by
Tyler Grimes
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-06-24
Latest Update: 2021-07-09
Description:
Methods to generate random gene-gene association networks and simulate RNA-seq data from them, as described in Grimes and Datta (2021) . Includes functions to generate random networks of any size and perturb them to obtain differential networks. Network objects are built from individual, overlapping modules that represent pathways. The resulting network has various topological properties that are characteristic of gene regulatory networks. RNA-seq data can be generated such that the association among gene expression profiles reflect the underlying network. A reference RNA-seq dataset can be provided to model realistic marginal distributions. Plotting functions are available to visualize a network, compare two networks, and compare the expression of two genes across multiple networks.
How to cite:
Tyler Grimes (2019). SeqNet: Generate RNA-Seq Data from Gene-Gene Association Networks. R package version 1.1.3, https://cran.r-project.org/web/packages/SeqNet. Accessed 18 Apr. 2025.
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Complete documentation for SeqNet
Functions, R codes and Examples using
the SeqNet R package
Some associated functions: add_modules_to_network . add_random_module_to_network . all_networks_contain_same_modules . all_networks_contain_same_nodes . 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.default . get_adjacency_matrix.matrix . get_adjacency_matrix.network . get_adjacency_matrix.network_module . get_adjacency_matrix . get_association_matrix.default . get_association_matrix.matrix . get_association_matrix.network . get_association_matrix.network_module . get_association_matrix . get_degree_distribution . get_edge_weights_from_module . get_layout_for_modules . get_network_arguments . get_network_characteristics . get_network_modules . get_node_names.default . get_node_names.matrix . get_node_names.network . get_node_names.network_module . get_node_names . get_sigma.default . get_sigma.matrix . get_sigma.network . get_sigma.network_module . get_sigma . get_summary_for_node . heatmap_network . is_PD . is_symmetric_cpp . is_weighted.default . is_weighted.matrix . is_weighted.network . is_weighted.network_module . is_weighted . perturb_network . plot.network . plot.network_module . plot.network_plot . plot_gene_pair . plot_modules . plot_network . plot_network_diff . plot_network_sim . print.network . print.network_module . print.network_plot . pzinb . qzinb . random_module . random_module_structure . random_network . reference . remove_connections.default . remove_connections.matrix . remove_connections.network . remove_connections.network_module . remove_connections . remove_connections_to_node.default . remove_connections_to_node.matrix . remove_connections_to_node.network . remove_connections_to_node.network_module . remove_connections_to_node . remove_weights.default . remove_weights.matrix . remove_weights.network . remove_weights.network_module . remove_weights . replace_module_in_network . rewire_connections.default . rewire_connections.matrix . rewire_connections.network . rewire_connections.network_module . rewire_connections . rewire_connections_to_node.default . rewire_connections_to_node.matrix . rewire_connections_to_node.network . rewire_connections_to_node.network_module . rewire_connections_to_node . ring_lattice_cpp . rzinb . sample_link_nodes . sample_module_nodes . sample_reference_data . set_module_edges . set_module_name . set_module_weights . set_node_names . update_module_with_random_weights .
Some associated R codes: RcppExports.R . cytoscape.R . data.R . gen_rnaseq.R . gen_zinb.R . generics.R . ggm.R . imports.R . misc.R . modules.R . networks.R . plotting.R . reference.R . Full SeqNet package functions and examples
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