Files in VladoBaca/BNRewiringRobustness
Discrete Bifurcation Analysis and Rewiring Robustness of Asynchronous Boolean Networks
.Rbuildignore
.gitignore
BNRewiringRobustness.Rproj
DESCRIPTION
LICENSE
NAMESPACE
R/attractors.R
R/bifurcation.R
R/extension.R
R/instance.R
R/io.R
R/parallelism.R
R/pbn.R
R/similarities.R
R/utils.R
README.md
inst/examples/basic.R
inst/examples/case_studies/1-inner/inner.R
inst/examples/case_studies/2-comparison/comparison.R
inst/examples/case_studies/3-extensions/e_coli.rg
inst/examples/case_studies/3-extensions/extension.R
inst/examples/case_studies/3-extensions/network_lower_case.txt
inst/examples/motifs/auto_minus.bn
inst/examples/motifs/auto_plus.bn
inst/examples/motifs/cellcycle_and.bn
inst/examples/motifs/cellcycle_or.bn
inst/examples/motifs/complex_test.bn
inst/examples/motifs/constant.bn
inst/examples/motifs/crm_and.bn
inst/examples/motifs/crm_assymetric.bn
inst/examples/motifs/crm_assymetric_left.bn
inst/examples/motifs/crm_assymetric_right.bn
inst/examples/motifs/crm_or.bn
inst/examples/motifs/eq_test.bn
inst/examples/motifs/fb_double_minus.bn
inst/examples/motifs/fb_minus.bn
inst/examples/motifs/fb_plus.bn
inst/examples/motifs/ffl_c1.bn
inst/examples/motifs/independent.bn
inst/examples/motifs/independent_auto_minus.bn
inst/examples/motifs/interesting.bn
inst/examples/motifs/mixed_regulated_double_minus.bn
inst/examples/motifs/nand.bn
inst/examples/motifs/test_triple_and.bn
inst/examples/motifs/test_triple_or.bn
inst/examples/motifs/two_attractors.bn
inst/examples/motifs/two_auto_minus.bn
inst/examples/motifs/weird.bn
inst/examples/motifs/xor.bn
inst/examples/rgs/all_reg_types.rg
inst/examples/rgs/extension_test.rg
inst/examples/rgs/general_1.rg
inst/examples/rgs/general_2.rg
inst/examples/rgs/general_3.rg
inst/examples/rgs/general_4.rg
inst/examples/rgs/general_5.rg
inst/examples/rgs/test_incorrect_multiple.rg
inst/examples/rgs/test_middle.rg
inst/examples/rgs/test_triple.rg
man/all_binary_vectors.Rd
man/bifurcation_plot.Rd
man/binary_vector_to_number.Rd
man/binary_vector_to_one_based_index.Rd
man/build_transition_table.Rd
man/compute_activity_ratios_matrix.Rd
man/compute_attractor_distribution_matrix.Rd
man/compute_attractor_distribution_similarity.Rd
man/compute_attractor_landscape_similarity.Rd
man/compute_attractor_membership_vector.Rd
man/compute_attractors_output_states_ratios_matrix.Rd
man/compute_attractors_similarity_matrix.Rd
man/compute_attractors_similarity_matrix_activity.Rd
man/compute_attractors_similarity_matrix_overlap.Rd
man/compute_constraints_coefficients_matrix.Rd
man/compute_conversion_vector.Rd
man/compute_db_single.Rd
man/compute_discrete_bifurcation.Rd
man/compute_discrete_bifurcation_inner.Rd
man/compute_intermediate_genes.Rd
man/compute_rewiring_distance.Rd
man/compute_rewiring_robustness.Rd
man/compute_transition_table_cell.Rd
man/compute_transition_table_row.Rd
man/create_extension.Rd
man/create_intermediate_motif_parametrisation.Rd
man/create_intermediate_rg.Rd
man/create_pbn_from_rg.Rd
man/decode_attractor.Rd
man/enumerate_gene_function_vectors.Rd
man/extract_instance.Rd
man/generate_BN.Rd
man/generate_interaction.Rd
man/generate_parametrisation_instance.Rd
man/get_attractor_landscape.Rd
man/get_attractors_data_async.Rd
man/get_attractors_data_sync.Rd
man/get_function_vector.Rd
man/get_parametrisation_by_index.Rd
man/get_parametrisation_by_index_combination_vector.Rd
man/get_rg_genes.Rd
man/is_function_vector_valid.Rd
man/is_simple_string.Rd
man/is_subset.Rd
man/load_BN.Rd
man/load_PBN.Rd
man/load_RG.Rd
man/parallel_apply.Rd
man/pre_to_post_vector.Rd
man/prepare_parallel.Rd
man/process_inputs.Rd
man/validate_edges.Rd
man/validate_genes.Rd
man/validate_unique_edges.Rd
tests/testthat.R
tests/testthat/test-attractors.R
tests/testthat/test-bifurcation.R
tests/testthat/test-extension.R
tests/testthat/test-instance.R
tests/testthat/test-io.R
tests/testthat/test-pbn.R
tests/testthat/test-similarities.R
tests/testthat/test-utils.R
