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abcdeFBA (version 0.2)

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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Version

Install

install.packages('abcdeFBA')

Monthly Downloads

16

Version

0.2

License

GPL-2

Maintainer

Abhilash Gangadharan

Last Published

January 22nd, 2012

Functions in abcdeFBA (0.2)

Ecoli_core.rda

E.coli core model 72 reactions and 95 metabolites
Ec_iAF1260_flux2

E.coli model 1260 ORF's
Ec_iJR904

E.coli model 904 ORF's
CHANGE_RXN_BOUNDS

CHANGE_RXN_BOUNDS, Change Reaction Bounds
flux_difference_plotter

flux_difference_plotter, a function to plot two pre-existing flux distributions obtained using FBA_solve
SEARCH_reaction

SEARCH_reaction, a function to search for reactions in a model using a simple text query
H_pylori_iIT341

Helicobacter pylori by Ines Thiele
SINGLE_DEL_FLUXOME

SINGLE_DEL_FLUXOME, a function to generate comparative fluxome graphs
H_sapien_Recon1

H. sapien Recon1, human metabolic network reconstruction
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
PHPP

PHPP, phenotypic phase plane analysis
Exhaustive_double_deletion

Exhaustive_double_deletion, a function for computing synthetic double knockouts.
Ec_iAF1260_flux1.rda

E.coli model 1260 ORF's
S_cerevisiae_IND750

Saccharomyces Cerevisiae iND750
BFD_Processor

BFD_Processor, a Bi-Flux-Del-Processor function
PERTURBATION_analysis

PERTURBATION_analysis, a function for robustness analysis.
M_barkeri_iAF629

Genome scale metabolic model for the archaeal methanogen M. Barkeri
DEGREE_MEASURE

DEGREE_MEASURE, measures the in-degree and out-degree of the metabolites in the network.
FLUX_VAR_ANALYSIS

FLUX_VAR_ANALYSIS, a function to perform a flux variability analysis.
Sybil_2_FBA_obj

Sybil_2_FBA_obj, a function to convert a model generated by Sybil into the one used by abcdeFBA.
FBA_solve

FBA_solve, a function to solve CBM problems
Gene_del

Gene_del, a function to create Gene Deletion mutants
M_tb_iNJ661

M. tuberculosis model iNJ661
SEARCH_metabolite

SEARCH_metabolite, a function to search for metabolites in a model using a simple text query
BYPASS_REACTIONS_SUBSTRATE

BYPASS_REACTIONS_SUBSTRATE, to find the influx and efflux reactions available to a particular metabolite/substrate
CHANGE_OBJ_FUNCTION

CHANGE_OBJ_FUNCTION, a function to change the objective for optimization
FVA_robustness

FVA_robustness, a function to determine the change in robustness of the network caused by a mutation.
S_aureus_iSB619

Staphylococcus aureus model iSB619 by S.Becker