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abcdeFBA (version 0.3)
ABCDE_FBA: A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package.
Description
Functions for Constraint Based Simulation using Flux Balance Analysis and informative analysis of the data generated during simulation.
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Install
install.packages('abcdeFBA')
Monthly Downloads
50
Version
0.3
License
GPL-2
Maintainer
Abhilash Gangadharan
Last Published
June 28th, 2012
Functions in abcdeFBA (0.3)
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Sybil_2_FBA_obj
Sybil_2_FBA_obj, a function to convert a model generated by Sybil into the one used by abcdeFBA.
FVA_robustness
FVA_robustness, a function to determine the change in robustness of the network caused by a mutation.
Exhaustive_double_deletion
Exhaustive_double_deletion, a function for computing synthetic double knockouts.
BYPASS_REACTIONS_SUBSTRATE
BYPASS_REACTIONS_SUBSTRATE, to find the influx and efflux reactions available to a particular metabolite/substrate
Ec_iAF1260_flux1.rda
E.coli model 1260 ORF's
S_cerevisiae_IND750
Saccharomyces Cerevisiae iND750
Ec_iJR904
E.coli model 904 ORF's
H_sapien_Recon1
H. sapien Recon1, human metabolic network reconstruction
Gene_del
Gene_del, a function to create Gene Deletion mutants
BFD_Processor
BFD_Processor, a Bi-Flux-Del-Processor function
flux_difference_plotter
flux_difference_plotter, a function to plot two pre-existing flux distributions obtained using FBA_solve
SEARCH_metabolite
SEARCH_metabolite, a function to search for metabolites in a model using a simple text query
PERTURBATION_analysis
PERTURBATION_analysis, a function for robustness analysis.
SINGLE_DEL_FLUXOME
SINGLE_DEL_FLUXOME, a function to generate comparative fluxome graphs
CHANGE_OBJ_FUNCTION
CHANGE_OBJ_FUNCTION, a function to change the objective for optimization
DEGREE_MEASURE
DEGREE_MEASURE, measures the in-degree and out-degree of the metabolites in the network.
View_objective
View_objective, a function that shows the components of the objective function.
Flux_Ranger
Flux_Ranger - a function to create a flux ramp.
FBA_solve
FBA_solve, a function to solve CBM problems
H_pylori_iIT341
Helicobacter pylori by Ines Thiele
CHANGE_RXN_BOUNDS
CHANGE_RXN_BOUNDS, Change Reaction Bounds
Ecoli_core.rda
E.coli core model 72 reactions and 95 metabolites
M_barkeri_iAF629
Genome scale metabolic model for the archaeal methanogen M. Barkeri
M_tb_iNJ661
M. tuberculosis model iNJ661
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
Ec_iAF1260_flux2
E.coli model 1260 ORF's
PHPP
PHPP, phenotypic phase plane analysis
FLUX_VAR_ANALYSIS
FLUX_VAR_ANALYSIS, a function to perform a flux variability analysis.
SEARCH_reaction
SEARCH_reaction, a function to search for reactions in a model using a simple text query
S_aureus_iSB619
Staphylococcus aureus model iSB619 by S.Becker