Package: SeqNet 1.1.3

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]

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SeqNet.pdf |SeqNet.html✨
SeqNet/json (API)

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

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

58 exports 0.71 score 37 dependencies 2 mentions 16 scripts 187 downloads

Last updated 3 years agofrom:1e333d06ae. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 14 2024
R-4.5-win-x86_64NOTESep 14 2024
R-4.5-linux-x86_64NOTESep 14 2024
R-4.4-win-x86_64NOTESep 14 2024
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Exports:add_random_module_to_networkas_single_modulecheck_adjacency_cppcomponents_in_adjacencyconnect_module_structurecreate_cytoscape_filecreate_empty_modulecreate_empty_networkcreate_module_from_adjacency_matrixcreate_module_from_association_matrixcreate_modules_for_networkcreate_network_from_adjacency_matrixcreate_network_from_association_matrixcreate_network_from_modulesdzinbecdf_cppedges_from_adjacency_cppest_params_from_referencegen_gaussiangen_partial_correlationsgen_rnaseqgen_zinbget_adjacency_matrixget_association_matrixget_degree_distributionget_edge_weights_from_moduleget_network_characteristicsget_network_modulesget_node_namesget_sigmaget_summary_for_nodeheatmap_networkis_symmetric_cppis_weightedperturb_networkplot_gene_pairplot_modulesplot_networkplot_network_diffplot_network_simpzinbqzinbrandom_modulerandom_module_structurerandom_networkremove_connectionsremove_connections_to_noderemove_weightsrewire_connectionsrewire_connections_to_nodering_lattice_cpprzinbsample_link_nodessample_module_nodessample_reference_dataset_module_nameset_node_namesupdate_module_with_random_weights

Dependencies:clicolorspacecpp11fansifarverfitdistrplusggplot2gluegtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellmvtnormnlmepillarpkgconfigpurrrR6rbibutilsRColorBrewerRcppRdpackrlangscalessurvivaltibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Internal function for adding a set of modules to the networkadd_modules_to_network
Adds a random module of a given size to the networkadd_random_module_to_network
Collapses all modules in network into a single moduleas_single_module
C++ implementation to check if a matrix is an adjacency matrixcheck_adjacency_cpp
C++ implementation to obtain connected components in a graph.components_in_adjacency
Connect disconnected components in an adjacency matrixconnect_module_structure
Create an edge table file for Cytoscapecreate_cytoscape_file
Create a modulecreate_empty_module
Create a network object.create_empty_network
Create a module from an adjacency matrixcreate_module_from_adjacency_matrix
Create a module from an association matrixcreate_module_from_association_matrix
Randomly sample subsets of genes for each modulecreate_modules_for_network
Create a network object from an adjacency matrixcreate_network_from_adjacency_matrix
Create a network object from an association matrixcreate_network_from_association_matrix
Create a network object.create_network_from_modules
The Zero-Inflated Negative Binomial Distributiondzinb
C++ implementation of empirical CDFecdf_cpp
C++ implementation for obtaining an edge list from adjacency matrixedges_from_adjacency_cpp
Estimate ZINB parameters from reference dataest_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 networkgen_rnaseq
Generate ZINB counts from an underlying networkgen_zinb
Get adjacency matrixget_adjacency_matrix
Get adjacency matrixget_adjacency_matrix.default
Get adjacency matrixget_adjacency_matrix.matrix
Get adjacency matrixget_adjacency_matrix.network
Get adjacency matrixget_adjacency_matrix.network_module
Get association matrixget_association_matrix
Get association matrixget_association_matrix.default
Get association matrixget_association_matrix.matrix
Get association matrixget_association_matrix.network
Get association matrixget_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 modulesget_layout_for_modules
Characteristics of the network topologyget_network_characteristics
Get a list of modules from the networkget_network_modules
Get node namesget_node_names
Get node namesget_node_names.default
Get node namesget_node_names.matrix
Get node namesget_node_names.network
Get node namesget_node_names.network_module
Get the covariance matrixget_sigma
Get the covariance matrixget_sigma.default
Get the covariance matrixget_sigma.matrix
Get the covariance matrixget_sigma.network
Get the covariance matrixget_sigma.network_module
Get summary for a node in the network.get_summary_for_node
Plot heatmap representation of a networkheatmap_network
C++ implementation to check if a matrix is symmetricis_symmetric_cpp
Check if an object is weightedis_weighted
Check if an object is weightedis_weighted.default
Check if an object is weightedis_weighted.matrix
Check if an object is weightedis_weighted.network
Check if an object is weightedis_weighted.network_module
Perturbs the connections in a networkperturb_network
Scatter plot of two gene expressionsplot_gene_pair
Visualize a network and its modulesplot_modules
Visualize a networkplot_network
Plot the difference between two networksplot_network_diff
Plot the similarity between two networksplot_network_sim
Plot function for 'network' objectplot.network
Plot function for 'network_module' object.plot.network_module
Plot function for 'network_plot' classplot.network_plot
Print function for 'network' object.print.network
Print function for 'network_module' object.print.network_module
Print function for 'network_plot' classprint.network_plot
The Zero-Inflated Negative Binomial Distributionpzinb
The Zero-Inflated Negative Binomial Distributionqzinb
Create a random modulerandom_module
Create a random network structure for a modulerandom_module_structure
Create a network object.random_network
RNA-seq reference datasetreference
Remove connections in a networkremove_connections
Remove connections to a noderemove_connections_to_node
Remove connections to a noderemove_connections_to_node.default
Remove connections to a noderemove_connections_to_node.matrix
Remove connections to a noderemove_connections_to_node.network
Remove connections to a noderemove_connections_to_node.network_module
Remove connections in a networkremove_connections.default
Remove connections in a networkremove_connections.matrix
Remove connections in a networkremove_connections.network
Remove connections in a networkremove_connections.network_module
Removes the weights of all connectionsremove_weights
Removes the weights of all connectionsremove_weights.default
Removes the weights of all connectionsremove_weights.matrix
Removes the weights of all connectionsremove_weights.network
Removes the weights of all connectionsremove_weights.network_module
Internal function for replacing a module in the networkreplace_module_in_network
Rewire connectionsrewire_connections
Rewire connections to a noderewire_connections_to_node
Rewire connections to a noderewire_connections_to_node.default
Rewire connections to a noderewire_connections_to_node.matrix
Rewire connections to a noderewire_connections_to_node.network
Rewire connections to a noderewire_connections_to_node.network_module
Rewire connectionsrewire_connections.default
Rewire connectionsrewire_connections.matrix
Rewire connectionsrewire_connections.network
Rewire connectionsrewire_connections.network_module
C++ implementation for creating a ring latticering_lattice_cpp
The Zero-Inflated Negative Binomial Distributionrzinb
Sample link nodes for new modulesample_link_nodes
Sample nodes for new modulesample_module_nodes
Sample genes from reference datasetsample_reference_data
Internal function used to set the edges in a moduleset_module_edges
Set the name for a moduleset_module_name
Internal function to set the connection weights for a moduleset_module_weights
Set the node names in a networkset_node_names
Generate small-world network structure for moduleupdate_module_with_random_weights