Package index

Core Functions

Main functions for metabolic flux analysis

calculate_reaction_score()

Calculate metabolic reaction scores (MRAS) for 13082 reactions

compute_flux()

Final optimization step for flux calculation

compute_sc_flux()

Single-Cell RNA-seq Metabolic Flux Calculation

calculate_avg_exp()

Calculate bootstrap mean expression for single cell data

Data

Built-in datasets

bulk_test_example

Bulk test example

sc_test_example

single cell test seurat object example

human_blood

This file contains the hams medium nutrients information in human blood

cell_medium

This file contains the hams medium nutrients information

human_gem

Human-GEM Metabolic Model Data

nutrient_lookup_files

1648 exchange reactions:mathematical representation of uptake/secrete metabolites into the extracellular space

Internal

Internal functions

construct_flux_bounds()

Construct flux bounds for OSQP optimization