Package: SeqNet 1.1.4

SeqNet: Generate RNA-Seq Data from Gene-Gene Association Networks

Methods to generate random gene-gene association networks and simulate RNA-seq data from them, as described in Grimes and Datta (2021) <doi:10.18637/jss.v098.i12>. 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.

Authors:Tyler Grimes [aut, cre], Somnath Datta [aut]

SeqNet_1.1.4.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
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SeqNet/json (API)

# Install 'SeqNet' in R:

install.packages('SeqNet', repos = c('https://tgrimes.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tgrimes/seqnet/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

reference - RNA-seq reference dataset

On CRAN:

cpp

5.18 score 6 stars 25 scripts 46 downloads 2 mentions 58 exports 33 dependencies

Last updated from:bf4e8b0786. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	149
linux-devel-x86_64	OK	128
source / vignettes	OK	252
linux-release-arm64	OK	142
linux-release-x86_64	OK	140
macos-release-arm64	OK	163
macos-release-x86_64	OK	373
macos-oldrel-arm64	OK	219
macos-oldrel-x86_64	OK	301
windows-devel-arm64	OK	380
windows-devel-x86_64	OK	148
windows-release-arm64	OK	354
windows-release-x86_64	OK	145
windows-oldrel-x86_64	OK	134
wasm-release	OK	111

Exports:add_random_module_to_network 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

Dependencies:cli cpp11 farver fitdistrplus ggplot2 glue gtable igraph isoband labeling lattice lifecycle magrittr MASS Matrix mvtnorm pillar pkgconfig purrr R6 rbibutils RColorBrewer Rcpp Rdpack rlang S7 scales survival tibble utf8 vctrs viridisLite withr

Introduction to SeqNet

Rendered fromSeqNet.Rmdusingknitr::rmarkdown

Last update: 2026-09-28
Started: 2026-09-28

Help page	Topics
Internal function for adding a set of modules to the network	add_modules_to_network
Adds a random module of a given size to the network	add_random_module_to_network
Collapses all modules in network into a single module	as_single_module
C++ implementation to check if a matrix is an adjacency matrix	check_adjacency_cpp
C++ implementation to obtain connected components in a graph.	components_in_adjacency
Connect disconnected components in an adjacency matrix	connect_module_structure
Create an edge table file for Cytoscape	create_cytoscape_file
Create a module	create_empty_module
Create a network object.	create_empty_network
Create a module from an adjacency matrix	create_module_from_adjacency_matrix
Create a module from an association matrix	create_module_from_association_matrix
Randomly sample subsets of genes for each module	create_modules_for_network
Create a network object from an adjacency matrix	create_network_from_adjacency_matrix
Create a network object from an association matrix	create_network_from_association_matrix
Create a network object.	create_network_from_modules
The Zero-Inflated Negative Binomial Distribution	dzinb
C++ implementation of empirical CDF	ecdf_cpp
C++ implementation for obtaining an edge list from adjacency matrix	edges_from_adjacency_cpp
Estimate ZINB parameters from reference data	est_params_from_reference
Generate observations from a Gaussian graphical model.	gen_gaussian
Generate partial correlations for a list of networks.	gen_partial_correlations
Generate RNA-seq data from an underlying network	gen_rnaseq
Generate ZINB counts from an underlying network	gen_zinb
Get adjacency matrix	get_adjacency_matrix
Get adjacency matrix	get_adjacency_matrix.default
Get adjacency matrix	get_adjacency_matrix.matrix
Get adjacency matrix	get_adjacency_matrix.network
Get adjacency matrix	get_adjacency_matrix.network_module
Get association matrix	get_association_matrix
Get association matrix	get_association_matrix.default
Get association matrix	get_association_matrix.matrix
Get association matrix	get_association_matrix.network
Get association matrix	get_association_matrix.network_module
Get the degree distribution for a network.	get_degree_distribution
Get edge weights.	get_edge_weights_from_module
Internal function used to create coordinates based on a set of modules	get_layout_for_modules
Characteristics of the network topology	get_network_characteristics
Get a list of modules from the network	get_network_modules
Get node names	get_node_names
Get node names	get_node_names.default
Get node names	get_node_names.matrix
Get node names	get_node_names.network
Get node names	get_node_names.network_module
Get the covariance matrix	get_sigma
Get the covariance matrix	get_sigma.default
Get the covariance matrix	get_sigma.matrix
Get the covariance matrix	get_sigma.network
Get the covariance matrix	get_sigma.network_module
Get summary for a node in the network.	get_summary_for_node
Plot heatmap representation of a network	heatmap_network
C++ implementation to check if a matrix is symmetric	is_symmetric_cpp
Check if an object is weighted	is_weighted
Check if an object is weighted	is_weighted.default
Check if an object is weighted	is_weighted.matrix
Check if an object is weighted	is_weighted.network
Check if an object is weighted	is_weighted.network_module
Perturbs the connections in a network	perturb_network
Scatter plot of two gene expressions	plot_gene_pair
Visualize a network and its modules	plot_modules
Visualize a network	plot_network
Plot the difference between two networks	plot_network_diff
Plot the similarity between two networks	plot_network_sim
Plot function for 'network' object	plot.network
Plot function for 'network_module' object.	plot.network_module
Plot function for 'network_plot' class	plot.network_plot
Print function for 'network' object.	print.network
Print function for 'network_module' object.	print.network_module
Print function for 'network_plot' class	print.network_plot
The Zero-Inflated Negative Binomial Distribution	pzinb
The Zero-Inflated Negative Binomial Distribution	qzinb
Create a random module	random_module
Create a random network structure for a module	random_module_structure
Create a network object.	random_network
RNA-seq reference dataset	reference
Remove connections in a network	remove_connections
Remove connections to a node	remove_connections_to_node
Remove connections to a node	remove_connections_to_node.default
Remove connections to a node	remove_connections_to_node.matrix
Remove connections to a node	remove_connections_to_node.network
Remove connections to a node	remove_connections_to_node.network_module
Remove connections in a network	remove_connections.default
Remove connections in a network	remove_connections.matrix
Remove connections in a network	remove_connections.network
Remove connections in a network	remove_connections.network_module
Removes the weights of all connections	remove_weights
Removes the weights of all connections	remove_weights.default
Removes the weights of all connections	remove_weights.matrix
Removes the weights of all connections	remove_weights.network
Removes the weights of all connections	remove_weights.network_module
Internal function for replacing a module in the network	replace_module_in_network
Rewire connections	rewire_connections
Rewire connections to a node	rewire_connections_to_node
Rewire connections to a node	rewire_connections_to_node.default
Rewire connections to a node	rewire_connections_to_node.matrix
Rewire connections to a node	rewire_connections_to_node.network
Rewire connections to a node	rewire_connections_to_node.network_module
Rewire connections	rewire_connections.default
Rewire connections	rewire_connections.matrix
Rewire connections	rewire_connections.network
Rewire connections	rewire_connections.network_module
C++ implementation for creating a ring lattice	ring_lattice_cpp
The Zero-Inflated Negative Binomial Distribution	rzinb
Sample link nodes for new module	sample_link_nodes
Sample nodes for new module	sample_module_nodes
Sample genes from reference dataset	sample_reference_data
Internal function used to set the edges in a module	set_module_edges
Set the name for a module	set_module_name
Internal function to set the connection weights for a module	set_module_weights
Set the node names in a network	set_node_names
Generate small-world network structure for module	update_module_with_random_weights

Package: SeqNet 1.1.4

SeqNet: Generate RNA-Seq Data from Gene-Gene Association Networks

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