Files in saezlab/CARNIVAL-Bioconductor-Dev
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
CARNIVAL.Rproj
DESCRIPTION
NAMESPACE
R/AddPerturbationNode.R
R/Uniprot2GeneSymbol.R
R/WriteDOTfig.R
R/all_constraints_wLoop.R
R/append_binaries.R
R/append_bounds.R
R/append_general_variables.R
R/append_objective_function.R
R/assignPROGENyScores.R
R/buildDataMatrix.R
R/checkInputObj.R
R/checkInputs.R
R/checkMeasObj.R
R/checkNetwork.R
R/checkSolver.R
R/checkSolverParam.R
R/checkWeightObj.R
R/cleanupCARNIVAL.R
R/controlNodeIdentifiers.R
R/createRegulonList.R
R/create_variables_all.R
R/exportResult.R
R/exportResultAllConditions.R
R/exportResultCBC.R
R/exportResultCPLEX.R
R/exportResultLPSolve.R
R/generateTFList.R
R/generate_measfile.R
R/genesymbol2uniprot.R
R/prepareLPMatrixSingle.R
R/runCARNIVAL.R
R/solveCARNIVAL.R
R/solveCARNIVALSingle.R
R/transformBinaries.R
R/transformBounds.R
R/transformConstraints.R
R/transformLPFile.R
R/transformObjectiveFunction.R
R/transformVariables.R
R/writeLPFile.R
R/writeLPFileMulti.R
R/writeSolverFiles.R
R/write_binaries.R
R/write_binaries_all_conditions.R
R/write_boundaries.R
R/write_boundaries_all_conditions.R
R/write_constraints_1.R
R/write_constraints_1_all.R
R/write_constraints_2.R
R/write_constraints_2_all.R
R/write_constraints_3.R
R/write_constraints_3_all.R
R/write_constraints_4.R
R/write_constraints_4_all.R
R/write_constraints_5.R
R/write_constraints_5_all.R
R/write_constraints_6.R
R/write_constraints_7.R
R/write_constraints_8.R
R/write_constraints_objFunction_all.R
R/write_experimental_conditions_constraints.R
R/write_generals.R
R/write_generals_all_conditions.R
R/write_loop_constraints.R
R/write_objective_function.R
R/write_objective_function_all.R
README.md
inst/progenyMembers.RData
inst/toy_inputs_ex1.RData
inst/toy_measurements_ex1.RData
inst/toy_measurements_ex2.RData
inst/toy_network_ex1.RData
inst/toy_network_ex2.RData
man/assignPROGENyScores.Rd
man/createRegulonList.Rd
man/generateTFList.Rd
man/runCARNIVAL.Rd
vignettes/.Rhistory
vignettes/ActivityNetwork_model_Nr0_Uniprot_page-0001.jpg
vignettes/CARNIVAL-vignette.Rnw
vignettes/Ex2_network_with_weights.jpeg
vignettes/Ex2_network_without_weights.jpeg
vignettes/apap_cbc.jpg
vignettes/apap_cplex.jpg
vignettes/carnival_pipeline.jpg
vignettes/carnival_vignette_toy.jpeg
vignettes/carnival_vignette_toy_2.jpeg
vignettes/egf_network.jpg
vignettes/real_case.jpg
vignettes/toy_network_ex1.jpeg
vignettes/toy_network_ex1_solution.jpeg
vignettes/toy_network_ex2.jpeg
vignettes/toy_network_ex2_solution.jpeg
