ABCDE_FBA: A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package.


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Documentation for package ‘abcdeFBA’ version 0.4

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alternative pathways BYPASS_REACTIONS_SUBSTRATE, to find the influx and efflux reactions available to a particular metabolite/substrate
BFD_Processor BFD_Processor, a Bi-Flux-Del-Processor function
bypass reactions for metabolites BYPASS_REACTIONS_SUBSTRATE, to find the influx and efflux reactions available to a particular metabolite/substrate
BYPASS_REACTIONS_SUBSTRATE BYPASS_REACTIONS_SUBSTRATE, to find the influx and efflux reactions available to a particular metabolite/substrate
change objective CHANGE_OBJ_FUNCTION, a function to change the objective for optimization
Change Reaction Bounds CHANGE_RXN_BOUNDS, Change Reaction Bounds
CHANGE_OBJ_FUNCTION CHANGE_OBJ_FUNCTION, a function to change the objective for optimization
CHANGE_RXN_BOUNDS CHANGE_RXN_BOUNDS, Change Reaction Bounds
comparison of single deletion flux distributions SINGLE_DEL_FLUXOME, a function to generate comparative fluxome graphs
degree-measure DEGREE_MEASURE, measures the in-degree and out-degree of the metabolites in the network.
DEGREE_MEASURE DEGREE_MEASURE, measures the in-degree and out-degree of the metabolites in the network.
double knockout Exhaustive_double_deletion, a function for computing synthetic double knockouts.
double knockout result processor BFD_Processor, a Bi-Flux-Del-Processor function
double synthetic lethality Exhaustive_double_deletion, a function for computing synthetic double knockouts.
Ecoli_core E.coli core model 72 reactions and 95 metabolites
Ec_iAF1260_flux1 E.coli model 1260 ORF's
Ec_iAF1260_flux2 E.coli model 1260 ORF's
Ec_iJR904 E.coli model 904 ORF's
Exhaustive_double_deletion Exhaustive_double_deletion, a function for computing synthetic double knockouts.
Exhaustive_single_deletion Exhaustive_single_deletion, a function that deletes each reaction in the network one at a time and returns results describing reaction lethality
FBA_solve FBA_solve, a function to solve CBM problems
flux distribution comparisons flux_difference_plotter, a function to plot two pre-existing flux distributions obtained using FBA_solve
Flux Variability Analysis FLUX_VAR_ANALYSIS, a function to perform a flux variability analysis.
fluxome graphs SINGLE_DEL_FLUXOME, a function to generate comparative fluxome graphs
flux_difference_plotter flux_difference_plotter, a function to plot two pre-existing flux distributions obtained using FBA_solve
Flux_Ranger Flux_Ranger - a function to create a flux ramp.
FLUX_VAR_ANALYSIS FLUX_VAR_ANALYSIS, a function to perform a flux variability analysis.
FVA_robustness FVA_robustness, a function to determine the change in robustness of the network caused by a mutation.
gene deletion Gene_del, a function to create Gene Deletion mutants
genetic mutants Gene_del, a function to create Gene Deletion mutants
Gene_del Gene_del, a function to create Gene Deletion mutants
H_pylori_iIT341 Helicobacter pylori by Ines Thiele
H_sapien_Recon1 H. sapien Recon1, human metabolic network reconstruction
in-degree DEGREE_MEASURE, measures the in-degree and out-degree of the metabolites in the network.
M_barkeri_iAF629 Genome scale metabolic model for the archaeal methanogen M. Barkeri
M_tb_iNJ661 M. tuberculosis model iNJ661
Objective function View_objective, a function that shows the components of the objective function.
objective function CHANGE_OBJ_FUNCTION, a function to change the objective for optimization
out-degree DEGREE_MEASURE, measures the in-degree and out-degree of the metabolites in the network.
parallel multi-core simulation Exhaustive_double_deletion, a function for computing synthetic double knockouts.
PERTURBATION_analysis PERTURBATION_analysis, a function for robustness analysis.
phenotypic phase plane analysis PHPP, phenotypic phase plane analysis
PHPP PHPP, phenotypic phase plane analysis
ramp-down PERTURBATION_analysis, a function for robustness analysis.
ramp-up PERTURBATION_analysis, a function for robustness analysis.
robustness analysis PERTURBATION_analysis, a function for robustness analysis.
Robustness analysis using FVA FVA_robustness, a function to determine the change in robustness of the network caused by a mutation.
SBML Sybil_2_FBA_obj, a function to convert a model generated by Sybil into the one used by abcdeFBA.
Search-metabolite SEARCH_metabolite, a function to search for metabolites in a model using a simple text query
Search-reaction SEARCH_reaction, a function to search for reactions in a model using a simple text query
SEARCH_metabolite SEARCH_metabolite, a function to search for metabolites in a model using a simple text query
SEARCH_reaction SEARCH_reaction, a function to search for reactions in a model using a simple text query
single knockouts Exhaustive_single_deletion, a function that deletes each reaction in the network one at a time and returns results describing reaction lethality
SINGLE_DEL_FLUXOME SINGLE_DEL_FLUXOME, a function to generate comparative fluxome graphs
solve FBA problem FBA_solve, a function to solve CBM problems
Sybil_2_FBA_obj Sybil_2_FBA_obj, a function to convert a model generated by Sybil into the one used by abcdeFBA.
Sybil_S4_object Sybil_2_FBA_obj, a function to convert a model generated by Sybil into the one used by abcdeFBA.
S_aureus_iSB619 Staphylococcus aureus model iSB619 by S.Becker
S_cerevisiae_IND750 Saccharomyces Cerevisiae iND750
View_objective View_objective, a function that shows the components of the objective function.