Man pages for DanielKneipp/DNAr
Simulates chemical reaction networks constructed with DNA
| add_gate_binding_on_neuron_hje | Add a gate binding into a neuron |
| analyze_behavior | This function returns the concentration derivative of each... |
| arg_list | Get the arguments of the current function |
| check_crn | Check if a CRN is respecting the limitations of the function... |
| check_fix_reaction | Check and fix a reaction |
| check_neuron_circuit_hje | Checks the circuit structure |
| check_neuron_gate_binding_hje | Check the gate binding structure |
| check_neuron_gate_hje | Checks the gate specification |
| check_reaction_4domain | Check if the reaction is compatible with the ones supported... |
| combine_crns | Combine CRNs into one single larger CRN |
| combine_reaction_parts | Combines two reaction parts to form a reaction |
| compare_behaviors_nrmse | Compare the behavior of two reactions |
| define_neuron_gate_binding_hje | Get the binding between two neuron gates |
| dsd_4d_make_module_str | Get a DSD 4domain module string |
| dsd_4d_modules | Get the available 4-domain modules for DSD script |
| dsd_4d_module_str | Returns a string with the 4-domain dsd module |
| eval_derivative | Evaluate a derivative returned by 'analyze_behavior()' |
| eval_derivative_part | Evaluate subexpressions of a derivative returned by... |
| expand_species | Function to expand species according to their stoichiometry |
| fte_theme | 'ggplot2' theme developed by Max Woolf. |
| get_buff_modules | Get buffer modules |
| get_circuit_from_neuron_gates_hje | Get a circuit from a list of gates |
| get_crn_from_neuron_circuit_hje | Get a CRN from a circuit |
| get_crn_from_neuron_gate_hje | Get a CRN given a gate |
| get_dsd_0eApBpC_str | Instantiate a '0 -> A + B + C' module in the DSD script |
| get_dsd_0eApB_str | Instantiate a '0 -> A + B' module in the DSD script |
| get_dsd_0eA_str | Instantiate a '0 -> A' module in the DSD script |
| get_dsd_4domain_modules_str | Get the 4-domain modules for the DSD script. |
| get_dsd_Ae0_str | Instantiate a 'A -> 0' module in the DSD script |
| get_dsd_AeBpCpD_str | Instantiate a 'A -> B + C + D' module in the DSD script |
| get_dsd_AeBpC_str | Instantiate a 'A -> B + C' module in the DSD script |
| get_dsd_AeB_str | Instantiate a 'A -> B' module in the DSD script |
| get_dsd_ApBe0_str | Instantiate a 'A + B -> 0' module in the DSD script |
| get_dsd_ApBeCpDpE_str | Instantiate a 'A + B -> C + D + E' module in the DSD script |
| get_dsd_ApBeCpD_str | Instantiate a 'A + B -> C + D' module in the DSD script |
| get_dsd_ApBeC_str | Instantiate a 'A + B -> C' module in the DSD script |
| get_dsd_buff_str | Instantiate a buffer module in the DSD script |
| get_dsd_def_str | Get a definition string for the DSD script |
| get_dsd_header_str | Get the DSD script header |
| get_dsd_species_str | Get the DSD definition of a species |
| get_first_part | Get the first part of a reaction. |
| get_M | Returns the matrix M. |
| get_neuron_AND_gate_hje | Get a AND neuron gate |
| get_neuron_binding_hje | Get a binding of two neurons |
| get_neuron_generic_gate_hje | Get a generic neuron gate with n inputs and 1 output |
| get_neuron_hje | Get a neuron based on Hjelmfelt A. et al. '[1]' approach |
| get_neuron_majority_gate | Get a majority gate |
| get_neuron_OR_gate_hje | Get a OR neuron gate |
| get_onespecies_count | Get the count of occurrences of a given species in a reaction... |
| get_products | Get the products of a given reaction |
| get_reactants | Get the reactants of a given reaction |
| get_second_part | Get the second part of a reaction. |
| get_species | Get the species of a reaction part |
| get_stoichiometry_all | Get the stoichiometry of a reaction |
| get_stoichiometry_onespecies | Get the stoichiometry of a specific species in a reaction. |
| get_stoichiometry_part | It returns the stoichiometry of part of a reaction. |
| is_bimolecular | Check if a reaction is bimolecular. |
| is_degradation | Check if a reaction is of the degradation type |
| isempty_part | Check if part of a reaction is equal to 0. |
| is_formation | Check if a reaction is of the formation type |
| is_unimolecular | Check if a reaction is unimolecular. |
| jn | Helper function to concatenate strings |
| load_behavior_csv | Load a reaction behavior |
| nrmse | Calculate the normalized root-mean-square error of two data... |
| plot_behavior | Plot the behavior of a CRN. |
| prepare_dsd_4d_module | Binds the module function with its parameters. |
| react | Simulate a CRN |
| react_4domain | Translate a formal CRN into a set of DNA based reactions... |
| reactants_in_reaction | Check which species are reactants in a given reaction |
| relation_operator | Gets the relation operator of the reaction |
| remove_stoichiometry | Remove the stoichiometry of a species string. |
| replace_module_markers | Replaces markers on a template string by other strings |
| rmse | Calculate the root-mean-square error of two data sets |
| save_behavior_csv | Save a reaction behavior |
| save_dsd_script | Export a DSD script for a CRN |
| save_reactions_txt | Save the reactions in a formatted text file |
| select_dsd_4d_module | Selects a module based on the reaction stoichiometry |
| update_crn_4domain | Automatically modify a CRN to make it compatible with the DNA... |
| update_neuron_input_hje | Update the neuron input according to the bindings |
