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.

Author
Abhilash Gangadharan, Neha Rohatgi
Date of publication
2012-09-15 13:13:26
Maintainer
Abhilash Gangadharan <gangutalk@gmail.com>
License
GPL-2
Version
0.4

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