An Extensible Approach to Flux Balance Analysis
Decompose a metabolite table into the metabolite stub itself and the c...
Parse a long format metabolic model to a glpk model
Parse a long format metabolic model to a Gurobi model
Convert intermediate expanded format back to a reaction table
Parse a long format metabolic model to an ROI model
fbar: Flux Balance Analysis in R with a tidy data approach
Given a metabolic model as a data frame, return a new data frame with ...
Given a metabolic model as a data frame, return a new data frame with ...
Apply gene expressions to reaction table
Function to estimate the expression levels of gene sets
Download a model from a BiGG json file
Internal function: Expand half reaction equations into a long form
Parse a reaction table to an intermediate, long format
Parse reaction table to Gurobi format
Merge metabolite stub and compartment to form an id
Internal function: Splitting reaction equation into substrate and prod...
Validate an expanded model
A toolkit for Flux Balance Analysis and related metabolic modeling techniques. Functions are provided for: parsing models in tabular format, converting parsed metabolic models to input formats for common linear programming solvers, and evaluating and applying gene-protein-reaction mappings. In addition, there are wrappers to parse a model, select a solver, find the metabolic fluxes, and return the results applied to the original model. Compared to other packages in this field, this package puts a much heavier focus on providing reusable components that can be used in the design of new implementation of new techniques, in particular those that involve large parameter sweeps. For a background on the theory, see What is Flux Balance Analysis <doi:10.1038/nbt.1614>.
Useful links