decompose_metabolites |
Decompose a metabolite table into the metabolite stub itself and the compartment it is in |
ecoli_core |
A small E. coli model, created from a number of sources. |
expanded_to_glpk |
Parse a long format metabolic model to a glpk model |
expanded_to_gurobi |
Parse a long format metabolic model to a Gurobi model |
expanded_to_reactiontbl |
Convert intermediate expanded format back to a reaction table |
expanded_to_ROI |
Parse a long format metabolic model to an ROI model |
fbar |
fbar: Flux Balance Analysis in R with a tidy data approach |
find_fluxes_df |
Given a metabolic model as a data frame, return a new data frame with fluxes |
find_flux_variability_df |
Given a metabolic model as a data frame, return a new data frame with fluxes and variability |
gene_associate |
Apply gene expressions to reaction table |
gene_eval |
Function to estimate the expression levels of gene sets |
get_BiGG |
Download a model from a BiGG json file |
iJO1366 |
A full size E. coli model. |
nutrient_types |
A subset of exchange reactions annotated to indicate typical availability |
parse_met_list |
Internal function: Expand half reaction equations into a long form |
reactiontbl_to_expanded |
Parse a reaction table to an intermediate, long format |
reactiontbl_to_gurobi |
Parse reaction table to Gurobi format |
recompose_metabolites |
Merge metabolite stub and compartment to form an id |
split_on_arrow |
Internal function: Splitting reaction equation into substrate and product |
validate_expanded |
Validate an expanded model |