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

Functions for Constraint Based Simulation using Flux Balance Analysis and informative analysis of the data generated during simulation.

AuthorAbhilash Gangadharan, Neha Rohatgi
Date of publication2012-09-15 13:13:26
MaintainerAbhilash Gangadharan <gangutalk@gmail.com>
LicenseGPL-2
Version0.4

View on CRAN

Man pages

BFDProcessor: BFD_Processor, a Bi-Flux-Del-Processor function

change_obj_function: CHANGE_OBJ_FUNCTION, a function to change the objective for...

change_rxn_bounds: CHANGE_RXN_BOUNDS, Change Reaction Bounds

deg_meas: DEGREE_MEASURE, measures the in-degree and out-degree of the...

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

Ecoli_core: E.coli core model 72 reactions and 95 metabolites

Exhaustive_double_deletion: Exhaustive_double_deletion, a function for computing...

Exhaustive_single_deletion: Exhaustive_single_deletion, a function that deletes each...

FBA_solve: FBA_solve, a function to solve CBM problems

fdiff: flux_difference_plotter, a function to plot two pre-existing...

flux_ranger: Flux_Ranger - a function to create a flux ramp.

fva: FLUX_VAR_ANALYSIS, a function to perform a flux variability...

fva_robustness: FVA_robustness, a function to determine the change in...

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

M_barkeri_iAF629: Genome scale metabolic model for the archaeal methanogen M....

metab_connect: BYPASS_REACTIONS_SUBSTRATE, to find the influx and efflux...

metab_srch: SEARCH_metabolite, a function to search for metabolites in a...

M_tb_iNJ661: M. tuberculosis model iNJ661

PERTURBATION_analysis: PERTURBATION_analysis, a function for robustness analysis.

PHPP: PHPP, phenotypic phase plane analysis

rxn_srch: SEARCH_reaction, a function to search for reactions in a...

S_aureus_iSB619: Staphylococcus aureus model iSB619 by S.Becker

S_cerevisiae_IND750: Saccharomyces Cerevisiae iND750

sing_del_flxme: SINGLE_DEL_FLUXOME, a function to generate comparative...

Sybil_2_FBA_obj: Sybil_2_FBA_obj, a function to convert a model generated by...

View_objective: View_objective, a function that shows the components of the...

Files in this package

abcdeFBA
abcdeFBA/NAMESPACE
abcdeFBA/R
abcdeFBA/R/metab_connect.R abcdeFBA/R/sybil2fba_object.R abcdeFBA/R/SINGLE_DEL_FLUXOME.R abcdeFBA/R/geneDel.R abcdeFBA/R/fva_robustness.R abcdeFBA/R/FBA_solve.R abcdeFBA/R/search_reaction_metabolite.R abcdeFBA/R/BFDProcessor.R abcdeFBA/R/Exhaustive_single_deletion.R abcdeFBA/R/View_objective.R abcdeFBA/R/PERTURBATION_analysis.R abcdeFBA/R/change_model.R abcdeFBA/R/flux_ranger.R abcdeFBA/R/Exhaustive_double_deletion.R abcdeFBA/R/PHPP.R abcdeFBA/R/flux_difference_plotter.R
abcdeFBA/man
abcdeFBA/man/Ecoli_core.Rd abcdeFBA/man/S_cerevisiae_IND750.Rd abcdeFBA/man/Exhaustive_single_deletion.Rd abcdeFBA/man/M_barkeri_iAF629.Rd abcdeFBA/man/H_pylori_iIT341.Rd abcdeFBA/man/PHPP.Rd abcdeFBA/man/BFDProcessor.Rd abcdeFBA/man/Ec_iAF1260_flux1.Rd abcdeFBA/man/metab_connect.Rd abcdeFBA/man/View_objective.Rd abcdeFBA/man/change_rxn_bounds.Rd abcdeFBA/man/Ec_iJR904.Rd abcdeFBA/man/deg_meas.Rd abcdeFBA/man/Sybil_2_FBA_obj.Rd abcdeFBA/man/FBA_solve.Rd abcdeFBA/man/sing_del_flxme.Rd abcdeFBA/man/fva_robustness.Rd abcdeFBA/man/M_tb_iNJ661.Rd abcdeFBA/man/Ec_iAF1260_flux2.Rd abcdeFBA/man/change_obj_function.Rd abcdeFBA/man/fva.Rd abcdeFBA/man/PERTURBATION_analysis.Rd abcdeFBA/man/flux_ranger.Rd abcdeFBA/man/Exhaustive_double_deletion.Rd abcdeFBA/man/fdiff.Rd abcdeFBA/man/S_aureus_iSB619.Rd abcdeFBA/man/rxn_srch.Rd abcdeFBA/man/metab_srch.Rd abcdeFBA/man/Gene_del.Rd abcdeFBA/man/H_sapien_Recon1.Rd
abcdeFBA/data
abcdeFBA/data/H_sapien_Recon1.rda
abcdeFBA/data/M_tb_iNJ661.rda
abcdeFBA/data/Ecoli_core.rda
abcdeFBA/data/M_barkeri_iAF629.rda
abcdeFBA/data/H_pylori_iIT341.rda
abcdeFBA/data/Ec_iAF1260_flux1.rda
abcdeFBA/data/Ec_iAF1260_flux2.rda
abcdeFBA/data/S_aureus_iSB619.rda
abcdeFBA/data/Ec_iJR904.rda
abcdeFBA/data/S_cerevisiae_IND750.rda
abcdeFBA/doc
abcdeFBA/doc/version_history
abcdeFBA/MD5
abcdeFBA/DESCRIPTION

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