Files in saezlab/CARNIVAL
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
.github/.gitignore
.github/ISSUE_TEMPLATE/issue_template.md
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/add_perturbation_node.R
R/api_run_carnival.R
R/check_inputs.R
R/check_measurements.R
R/check_perturbations.R
R/check_prior_knowledge_network.R
R/check_solver_param.R
R/check_weights.R
R/cleanup_carnival.R
R/constraints_auxilliary.R
R/constraints_create_constraints_1_2_3.R
R/constraints_create_constraints_4_5.R
R/constraints_create_constraints_6_7.R
R/constraints_create_constraints_8.R
R/constraints_create_constraints_measurements.R
R/constraints_create_loop_constraints.R
R/control_node_identifiers.R
R/create_lp_formulation.R
R/create_objective_function.R
R/create_run_metainfo.R
R/create_variables.R
R/prune_network.R
R/set_carnival_options.R
R/set_solver_path.R
R/solve_carnival.R
R/solvers_cbc__solve_cbc.R
R/solvers_cplex__parse_cplex_log.R
R/solvers_cplex__solve_cplex.R
R/solvers_cplex__write_cplex_command_file.R
R/solvers_export_results.R
R/solvers_gurobi__solve_gurobi.R
R/solvers_lpsolve__prepare_lp_matrix_single.R
R/solvers_lpsolve__solve_lpsolve.R
R/solvers_lpsolve__transform_binaries.R
R/solvers_lpsolve__transform_bounds.R
R/solvers_lpsolve__transform_constraints.R
R/solvers_lpsolve__transform_objective_function.R
R/solvers_lpsolve__transform_variables.R
R/sysdata.rda
R/write_solver_files.R
README.Rmd
README.md
codecov.yml
docs/404.html
docs/articles/CARNIVAL.html
docs/articles/index.html
docs/articles/vignettes_pictures/graphical_abstract.png
docs/authors.html
docs/index.html
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/addPerturbationNodes.html
docs/reference/checkCarnivalOptions.html
docs/reference/checkData.html
docs/reference/checkOptionsValidity.html
docs/reference/checkPriorKnowledgeNetwork.html
docs/reference/createInternalDataRepresentation.html
docs/reference/defaultCbcSolveCarnivalOptions.html
docs/reference/defaultCplexCarnivalOptions.html
docs/reference/defaultCplexSpecificOptions.html
docs/reference/defaultLpSolveCarnivalOptions.html
docs/reference/generateLpFileCarnival.html
docs/reference/getOptionsList.html
docs/reference/getSupportedSolvers.html
docs/reference/getSupportedSolversFunctions.html
docs/reference/index.html
docs/reference/isInputValidCarnival.html
docs/reference/parseCplexLog.html
docs/reference/prepareForCarnivalRun.html
docs/reference/preprocessPriorKnowledgeNetwork.html
docs/reference/processSolution.html
docs/reference/readOptions.html
docs/reference/runCARNIVAL.html
docs/reference/runFromLpCarnival.html
docs/reference/runInverseCarnival.html
docs/reference/runVanillaCarnival.html
docs/reference/sendTaskToSolver.html
docs/reference/setCarnivalOptions.html
docs/reference/solveCarnival.html
docs/reference/solveCarnivalFromLp.html
docs/reference/solveWithCbc.html
docs/reference/suggestedCbcSpecificOptions.html
docs/reference/suggestedCplexSpecificOptions.html
docs/reference/writeParsedData.html
for_developers/Updates_presentation.pptx
inst/CITATION
inst/carnival_cplex_parameters.json
inst/progenyMembers.RData
inst/simpleIlpProblem.lp
inst/toy_inputs_ex1.RData
inst/toy_lp_file_ex1.lp
inst/toy_measurements_ex1.RData
inst/toy_measurements_ex2.RData
inst/toy_network_ex1.RData
inst/toy_network_ex2.RData
inst/toy_parsed_data_ex1.RData
inst/toy_perturbations_ex1.RData
inst/toy_result_expected_ex1.RData
man/addPerturbationNodes.Rd
man/checkCarnivalOptions.Rd
man/checkData.Rd
man/checkOptionsValidity.Rd
man/checkPriorKnowledgeNetwork.Rd
man/createInternalDataRepresentation.Rd
man/defaultCbcSolveCarnivalOptions.Rd
man/defaultCplexCarnivalOptions.Rd
man/defaultCplexSpecificOptions.Rd
man/defaultLpSolveCarnivalOptions.Rd
man/figures/graphical_abstract.png
man/generateLpFileCarnival.Rd
man/getOptionsList.Rd
man/getSupportedSolvers.Rd
man/getSupportedSolversFunctions.Rd
man/isInputValidCarnival.Rd
man/parseCplexLog.Rd
man/prepareForCarnivalRun.Rd
man/preprocessPriorKnowledgeNetwork.Rd
man/processSolution.Rd
man/prune_network.Rd
man/readOptions.Rd
man/runCARNIVAL.Rd
man/runFromLpCarnival.Rd
man/runInverseCarnival.Rd
man/runVanillaCarnival.Rd
man/searchForCPLEXSolver.Rd
man/sendTaskToSolver.Rd
man/setCarnivalOptions.Rd
man/solveCarnival.Rd
man/solveCarnivalFromLp.Rd
man/solveWithCbc.Rd
man/solveWithGurobi.Rd
man/suggestedCbcSpecificOptions.Rd
man/suggestedCplexSpecificOptions.Rd
man/testRunCplex.Rd
man/writeCplexCommandFileFromJson.Rd
man/writeParsedData.Rd
parameters/README.md
parameters/carnival_cbc_parameters.json
parameters/carnival_cplex_parameters.json
parameters/carnival_cplex_parameters_mine.json
parameters/carnival_gurobi_parameters.json
parameters/carnival_lpsolve_parameters.json
parameters/cplex_parameters_cmd_file.json
tests/testthat.R
tests/testthat/create_dummy_data_n.R
tests/testthat/temp_create_dummy_data.R
tests/testthat/test-set_solver_path.R
tests/testthat/test_carnival_simplest_case.R
tests/testthat/test_cbc_small_models.R
tests/testthat/test_constraint_1_2.R
tests/testthat/test_constraint_3.R
tests/testthat/test_constraint_4_5.R
tests/testthat/test_constraint_6_7.R
tests/testthat/test_constraint_8.R
tests/testthat/test_control_node_identifiers.R
tests/testthat/test_cplex_small_models.R
tests/testthat/test_createEdgesVariables.R
tests/testthat/test_createMeasurementsVariables.R
tests/testthat/test_createNodesVariables.R
tests/testthat/test_gurobi_small_models.R
tests/testthat/test_integration.R
tests/testthat/test_inverseCarnival.R
tests/testthat/test_lpSolve_small_models.R
tests/testthat/test_parse_cplex_log.R
tests/testthat/test_weights.R
tests/testthat/tests_preprocessPriorKnowledgeNetwork.R
vignettes/.gitignore
vignettes/CARNIVAL-vignette.pdf
vignettes/CARNIVAL.Rmd
vignettes/CARNIVAL.html
vignettes/toy_files_vignettes/lpFile_t18_01_53d28_04_2021n4.lp
vignettes/toy_files_vignettes/parsedData_t18_01_53d28_04_2021n4.RData
vignettes/vignettes_pictures/graphical_abstract.png
