An Extensible Approach to Flux Balance Analysis

Documentation for package ‘fbar’ version 0.6.0

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