| as.graph | Converts a reaction list into a graph object. |
| as.reactions | Converts a stochiometric matrix to a reaction list. |
| as.stability | Translates the eigenvectors to the corresponding stability... |
| closest | Finds the closest point in within the k-cone to a query point... |
| constant_flux | Identifies reactions with a constant flux, thus reactions... |
| constrain_by_Keq | Get the equality constraints for a given set of known... |
| deriv_ma | Calculates derivatives of mass-action kinetics. |
| dycone | dycone: Differential k-cone analysis for metabolome data. |
| eigendynamics | Gets the eigendynamics for a given k.cone basis. |
| enorm | Calculates the euclidean norm of a vector |
| eryth | Metabolic network of human red blood cell. |
| fba | Maximizes the flux through a given objective reaction. |
| find_hmdb | Finds IDs of compounds from HMDB corresponding to a given... |
| fva | Performs flux variance analysis for a given objective... |
| grapes-c-grapes | expression, detects all assigned variables and saves them... |
| grep_id | Wrapper for grep that returns NA if nothing was found. Also... |
| hmdb_concentration | Scrapes measured metabolite concentration values for a given... |
| hmdb_parse_concentration | Parses basic data from a set of HMDB concentration nodes. |
| hmdb_parse_xml | Parses the XML entry for a single HMDB id |
| hyp | Identifies hypothesis for differentially regulated reactions... |
| inside | Evaluates whether a given point lies within a given k-cone.... |
| jacobian | Calculates the Jacobian matrix. |
| kcone | Get the k-cone from a given flux cone. |
| kcone_null | Gets the null-space for the given k-cone assuming that all... |
| make_irreversible | Converts a given reaction list into an irreversible one,... |
| mass_action | Calculates a mass-action reaction rate |
| ma_terms | Calculates all mass action terms prod_{i \in N^-} S_i^|N_i| |
| minimal_perturbation | Assemble the LP problem for minimal perturbation. |
| minimal_perturbation_lp | Assemble the LP problem for minimal perturbation. |
| occupation | Calculates the occupation for a basis. Here, occupation... |
| parse_conc | Parses concentration values from HMDB. |
| patch | Patches holes in a data set by using group means and... |
| pfba | Maximizes a set of given fluxes within the k-cone using... |
| plot_basis | Plots a heatmap of the basis. |
| plot.reactions | Plots the reactions as a graph. |
| plot_red | Plots a geometric visualization of the given k-cone reduced... |
| polytope_basis | Gets the polytope basis for a reaction system. The basis will... |
| print.reactions | Prints a nice description of the reactions. |
| priority_mean | Extracts mean concentrations from HMDB results using a... |
| read_reactions | Reads a list of reactions with optional annotations from a... |
| read_sbml | Main driver to parse an SBML model. |
| r_order | Returns the number of different substrates a reaction has |
| rp | Obtains properties from a reaction list |
| sbml_params | Obtains the list of parameters from a SBML model |
| sbml_reactions | Obtains the list of reactions from a SBML file. |
| sbml_species | Obtains the list of species from a SBML model |
| single_hyp | Helper function to get the differential regulation between... |
| species | Gets all species/metabolites from a reaction list. |
| stability_analysis | Performs a stability analysis for each basis vector in a... |
| stoichiometry | Calculates the stochiometric matrix for a list of reactions. |
| timecourse | Simulates the time course for a given model. |
| which_reaction | Finds all reaction indices using the given subtrates and... |
