dycone - analyze the dynamic landscape of metabolome data

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... |

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