Files in DanielKneipp/DNAr
Simulates chemical reaction networks constructed with DNA
.Rbuildignore
.gitignore
.travis.yml
4-domain To R.Rproj
DESCRIPTION
LICENSE.md
NAMESPACE
R/4domain_reactor.R
R/analysis.R
R/crn_reactor.R
R/dsd.R
R/io.R
R/neuron_hjelmfelt.R
R/parser.R
README.md
README_assets/bi_dna.png
README_assets/dnar_vdsd_workflow_eng.png
README_assets/dsd_main.png
README_assets/dsd_reacs.png
README_assets/neuron01.png
README_assets/neuron_0.png
README_assets/neuron_1.png
README_assets/uni.png
demo/00Index
demo/main_4domain.R
demo/main_crn.R
inst/REFERENCES.bib
man/add_gate_binding_on_neuron_hje.Rd
man/analyze_behavior.Rd
man/arg_list.Rd
man/check_crn.Rd
man/check_fix_reaction.Rd
man/check_neuron_circuit_hje.Rd
man/check_neuron_gate_binding_hje.Rd
man/check_neuron_gate_hje.Rd
man/check_reaction_4domain.Rd
man/combine_crns.Rd
man/combine_reaction_parts.Rd
man/compare_behaviors_nrmse.Rd
man/define_neuron_gate_binding_hje.Rd
man/dsd_4d_make_module_str.Rd
man/dsd_4d_module_str.Rd
man/dsd_4d_modules.Rd
man/eval_derivative.Rd
man/eval_derivative_part.Rd
man/expand_species.Rd
man/fte_theme.Rd
man/get_M.Rd
man/get_buff_modules.Rd
man/get_circuit_from_neuron_gates_hje.Rd
man/get_crn_from_neuron_circuit_hje.Rd
man/get_crn_from_neuron_gate_hje.Rd
man/get_dsd_0eA_str.Rd
man/get_dsd_0eApB_str.Rd
man/get_dsd_0eApBpC_str.Rd
man/get_dsd_4domain_modules_str.Rd
man/get_dsd_Ae0_str.Rd
man/get_dsd_AeB_str.Rd
man/get_dsd_AeBpC_str.Rd
man/get_dsd_AeBpCpD_str.Rd
man/get_dsd_ApBe0_str.Rd
man/get_dsd_ApBeC_str.Rd
man/get_dsd_ApBeCpD_str.Rd
man/get_dsd_ApBeCpDpE_str.Rd
man/get_dsd_buff_str.Rd
man/get_dsd_def_str.Rd
man/get_dsd_header_str.Rd
man/get_dsd_species_str.Rd
man/get_first_part.Rd
man/get_neuron_AND_gate_hje.Rd
man/get_neuron_OR_gate_hje.Rd
man/get_neuron_binding_hje.Rd
man/get_neuron_generic_gate_hje.Rd
man/get_neuron_hje.Rd
man/get_neuron_majority_gate.Rd
man/get_onespecies_count.Rd
man/get_products.Rd
man/get_reactants.Rd
man/get_second_part.Rd
man/get_species.Rd
man/get_stoichiometry_all.Rd
man/get_stoichiometry_onespecies.Rd
man/get_stoichiometry_part.Rd
man/is_bimolecular.Rd
man/is_degradation.Rd
man/is_formation.Rd
man/is_unimolecular.Rd
man/isempty_part.Rd
man/jn.Rd
man/load_behavior_csv.Rd
man/nrmse.Rd
man/plot_behavior.Rd
man/prepare_dsd_4d_module.Rd
man/react.Rd
man/react_4domain.Rd
man/reactants_in_reaction.Rd
man/relation_operator.Rd
man/remove_stoichiometry.Rd
man/replace_module_markers.Rd
man/rmse.Rd
man/save_behavior_csv.Rd
man/save_dsd_script.Rd
man/save_reactions_txt.Rd
man/select_dsd_4d_module.Rd
man/update_crn_4domain.Rd
man/update_neuron_input_hje.Rd
tests/testthat.R
tests/testthat/data/3prod.dsd
tests/testthat/data/AeBpC.dsd
tests/testthat/data/ApBeC.dsd
tests/testthat/data/behavior_0e2A_4domain.csv
tests/testthat/data/behavior_0eA.csv
tests/testthat/data/behavior_0eA_4domain.csv
tests/testthat/data/behavior_0eApB_4domain.csv
tests/testthat/data/behavior_2Ae0_4domain.csv
tests/testthat/data/behavior_2Ae2B.csv
tests/testthat/data/behavior_2Ae2BpA.csv
tests/testthat/data/behavior_3prod_4domain.csv
tests/testthat/data/behavior_Ae0.csv
tests/testthat/data/behavior_Ae0_4domain.csv
tests/testthat/data/behavior_Ae2B.csv
tests/testthat/data/behavior_AeB_4domain.csv
tests/testthat/data/behavior_ApBe0_4domain.csv
tests/testthat/data/behavior_ApBeC.csv
tests/testthat/data/behavior_ApBeC_4d.csv
tests/testthat/data/behavior_ApBeC_4domain.csv
tests/testthat/data/behavior_consensus.csv
tests/testthat/data/behavior_consensus_4domain.csv
tests/testthat/data/behavior_lotka.csv
tests/testthat/data/behavior_lotka_4domain.csv
tests/testthat/data/consensus.dsd
tests/testthat/data/consensus.txt
tests/testthat/data/dummy1.dsd
tests/testthat/data/dummy2.dsd
tests/testthat/data/dummy_behavior.csv
tests/testthat/data/neuron_hje/neuron_hje_AND_00.csv
tests/testthat/data/neuron_hje/neuron_hje_AND_01.csv
tests/testthat/data/neuron_hje/neuron_hje_AND_10.csv
tests/testthat/data/neuron_hje/neuron_hje_AND_11.csv
tests/testthat/data/neuron_hje/neuron_hje_AND_AND_000.csv
tests/testthat/data/neuron_hje/neuron_hje_AND_AND_001.csv
tests/testthat/data/neuron_hje/neuron_hje_AND_AND_011.csv
tests/testthat/data/neuron_hje/neuron_hje_AND_AND_111.csv
tests/testthat/data/neuron_hje/neuron_hje_MAJ_3i.csv
tests/testthat/data/neuron_hje/neuron_hje_MAJ_5i.csv
tests/testthat/data/neuron_hje/neuron_hje_MAJ_7i.csv
tests/testthat/data/neuron_hje/neuron_hje_activated.csv
tests/testthat/data/neuron_hje/neuron_hje_deactivated.csv
tests/testthat/test_4domain_behavior.R
tests/testthat/test_analysis.R
tests/testthat/test_crn_behavior.R
tests/testthat/test_crn_parser.R
tests/testthat/test_dsd_export.R
tests/testthat/test_io.R
tests/testthat/test_neuron_hje.R
