Files in tgrimes/SeqNet
Generate RNA-Seq Data from Gene-Gene Association Networks
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/RcppExports.R
R/cytoscape.R
R/data.R
R/gen_rnaseq.R
R/gen_zinb.R
R/generics.R
R/ggm.R
R/imports.R
R/misc.R
R/modules.R
R/networks.R
R/plotting.R
R/reference.R
README.md
SeqNet.Rproj
data/reference.rda
man/add_modules_to_network.Rd
man/add_random_module_to_network.Rd
man/all_networks_contain_same_modules.Rd
man/all_networks_contain_same_nodes.Rd
man/as_single_module.Rd
man/components_in_adjacency.Rd
man/connect_module_structure.Rd
man/create_cytoscape_file.Rd
man/create_empty_module.Rd
man/create_empty_network.Rd
man/create_module_from_adjacency_matrix.Rd
man/create_module_from_association_matrix.Rd
man/create_modules_for_network.Rd
man/create_network_from_adjacency_matrix.Rd
man/create_network_from_association_matrix.Rd
man/create_network_from_modules.Rd
man/dzinb.Rd
man/ecdf_cpp.Rd
man/edges_from_adjacency_cpp.Rd
man/est_params_from_reference.Rd
man/gen_gaussian.Rd
man/gen_partial_correlations.Rd
man/gen_rnaseq.Rd
man/gen_zinb.Rd
man/get_adjacency_matrix.Rd
man/get_adjacency_matrix.default.Rd
man/get_adjacency_matrix.matrix.Rd
man/get_adjacency_matrix.network.Rd
man/get_adjacency_matrix.network_module.Rd
man/get_association_matrix.Rd
man/get_association_matrix.default.Rd
man/get_association_matrix.matrix.Rd
man/get_association_matrix.network.Rd
man/get_association_matrix.network_module.Rd
man/get_degree_distribution.Rd
man/get_edge_weights_from_module.Rd
man/get_layout_for_modules.Rd
man/get_network_arguments.Rd
man/get_network_characteristics.Rd
man/get_network_modules.Rd
man/get_node_names.Rd
man/get_node_names.default.Rd
man/get_node_names.matrix.Rd
man/get_node_names.network.Rd
man/get_node_names.network_module.Rd
man/get_sigma.Rd
man/get_sigma.default.Rd
man/get_sigma.matrix.Rd
man/get_sigma.network.Rd
man/get_sigma.network_module.Rd
man/get_summary_for_node.Rd
man/heatmap_network.Rd
man/is_PD.Rd
man/is_adjacency_cpp.Rd
man/is_symmetric_cpp.Rd
man/is_weighted.Rd
man/is_weighted.default.Rd
man/is_weighted.matrix.Rd
man/is_weighted.network.Rd
man/is_weighted.network_module.Rd
man/perturb_network.Rd
man/plot.network.Rd
man/plot.network_module.Rd
man/plot.network_plot.Rd
man/plot_gene_pair.Rd
man/plot_modules.Rd
man/plot_network.Rd
man/plot_network_diff.Rd
man/plot_network_sim.Rd
man/print.network.Rd
man/print.network_module.Rd
man/print.network_plot.Rd
man/pzinb.Rd
man/qzinb.Rd
man/random_module.Rd
man/random_module_structure.Rd
man/random_network.Rd
man/reference.Rd
man/remove_connections.Rd
man/remove_connections.default.Rd
man/remove_connections.matrix.Rd
man/remove_connections.network.Rd
man/remove_connections.network_module.Rd
man/remove_connections_to_node.Rd
man/remove_connections_to_node.default.Rd
man/remove_connections_to_node.matrix.Rd
man/remove_connections_to_node.network.Rd
man/remove_connections_to_node.network_module.Rd
man/remove_weights.Rd
man/remove_weights.default.Rd
man/remove_weights.matrix.Rd
man/remove_weights.network.Rd
man/remove_weights.network_module.Rd
man/replace_module_in_network.Rd
man/rewire_connections.Rd
man/rewire_connections.default.Rd
man/rewire_connections.matrix.Rd
man/rewire_connections.network.Rd
man/rewire_connections.network_module.Rd
man/rewire_connections_to_node.Rd
man/rewire_connections_to_node.default.Rd
man/rewire_connections_to_node.matrix.Rd
man/rewire_connections_to_node.network.Rd
man/rewire_connections_to_node.network_module.Rd
man/ring_lattice_cpp.Rd
man/rzinb.Rd
man/sample_link_nodes.Rd
man/sample_module_nodes.Rd
man/sample_reference_data.Rd
man/set_module_edges.Rd
man/set_module_name.Rd
man/set_module_weights.Rd
man/set_node_names.Rd
man/update_module_with_random_weights.Rd
src/.gitignore
src/RcppExports.cpp
src/components_in_adjacency.cpp
src/ecdf.cpp
src/edges_from_adjacency.cpp
src/is_adjacency.cpp
src/is_symmetric.cpp
src/ring_lattice.cpp
tests/testthat.R
tests/testthat/test_cpp_functions.R
tests/testthat/test_create_network.R
tests/testthat/test_gen_counts.R
tests/testthat/test_network_node_names.R
tests/testthat/test_network_structure.R
tests/testthat/test_qzinb.R
tests/testthat/test_random_network.R
tests/testthat/test_sigma_matrix.R
