Man pages for cdiener/dycone
dycone - analyze the dynamic landscape of metabolome data

as.graphConverts a reaction list into a graph object.
as.reactionsConverts a stochiometric matrix to a reaction list.
as.stabilityTranslates the eigenvectors to the corresponding stability...
closestFinds the closest point in within the k-cone to a query point...
constant_fluxIdentifies reactions with a constant flux, thus reactions...
constrain_by_KeqGet the equality constraints for a given set of known...
deriv_maCalculates derivatives of mass-action kinetics.
dyconedycone: Differential k-cone analysis for metabolome data.
eigendynamicsGets the eigendynamics for a given k.cone basis.
enormCalculates the euclidean norm of a vector
erythMetabolic network of human red blood cell.
fbaMaximizes the flux through a given objective reaction.
find_hmdbFinds IDs of compounds from HMDB corresponding to a given...
fvaPerforms flux variance analysis for a given objective...
grapes-c-grapesexpression, detects all assigned variables and saves them...
grep_idWrapper for grep that returns NA if nothing was found. Also...
hmdb_concentrationScrapes measured metabolite concentration values for a given...
hmdb_parse_concentrationParses basic data from a set of HMDB concentration nodes.
hmdb_parse_xmlParses the XML entry for a single HMDB id
hypIdentifies hypothesis for differentially regulated reactions...
insideEvaluates whether a given point lies within a given k-cone....
jacobianCalculates the Jacobian matrix.
kconeGet the k-cone from a given flux cone.
kcone_nullGets the null-space for the given k-cone assuming that all...
make_irreversibleConverts a given reaction list into an irreversible one,...
mass_actionCalculates a mass-action reaction rate
ma_termsCalculates all mass action terms prod_{i \in N^-} S_i^|N_i|
minimal_perturbationAssemble the LP problem for minimal perturbation.
minimal_perturbation_lpAssemble the LP problem for minimal perturbation.
occupationCalculates the occupation for a basis. Here, occupation...
parse_concParses concentration values from HMDB.
patchPatches holes in a data set by using group means and...
pfbaMaximizes a set of given fluxes within the k-cone using...
plot_basisPlots a heatmap of the basis.
plot.reactionsPlots the reactions as a graph.
plot_redPlots a geometric visualization of the given k-cone reduced...
polytope_basisGets the polytope basis for a reaction system. The basis will...
print.reactionsPrints a nice description of the reactions.
priority_meanExtracts mean concentrations from HMDB results using a...
read_reactionsReads a list of reactions with optional annotations from a...
read_sbmlMain driver to parse an SBML model.
r_orderReturns the number of different substrates a reaction has
rpObtains properties from a reaction list
sbml_paramsObtains the list of parameters from a SBML model
sbml_reactionsObtains the list of reactions from a SBML file.
sbml_speciesObtains the list of species from a SBML model
single_hypHelper function to get the differential regulation between...
speciesGets all species/metabolites from a reaction list.
stability_analysisPerforms a stability analysis for each basis vector in a...
stoichiometryCalculates the stochiometric matrix for a list of reactions.
timecourseSimulates the time course for a given model.
which_reactionFinds all reaction indices using the given subtrates and...
cdiener/dycone documentation built on Sept. 9, 2018, 1:20 p.m.