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.

Install the latest version of this package by entering the following in R:
install.packages("abcdeFBA")
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...

Functions

alternative pathways Man page
BFD_Processor Man page
bypass reactions for metabolites Man page
BYPASS_REACTIONS_SUBSTRATE Man page
change objective Man page
CHANGE_OBJ_FUNCTION Man page
Change Reaction Bounds Man page
CHANGE_RXN_BOUNDS Man page
comparison of single deletion flux distributions Man page
degree-measure Man page
DEGREE_MEASURE Man page
double knockout Man page
double knockout result processor Man page
double synthetic lethality Man page
Ec_iAF1260_flux1 Man page
Ec_iAF1260_flux2 Man page
Ec_iJR904 Man page
Ecoli_core Man page
Exhaustive_double_deletion Man page
Exhaustive_single_deletion Man page
FBA_solve Man page
flux_difference_plotter Man page
flux distribution comparisons Man page
fluxome graphs Man page
Flux_Ranger Man page
FLUX_VAR_ANALYSIS Man page
Flux Variability Analysis Man page
FVA_robustness Man page
Gene_del Man page
gene deletion Man page
genetic mutants Man page
H_pylori_iIT341 Man page
H_sapien_Recon1 Man page
in-degree Man page
M_barkeri_iAF629 Man page
M_tb_iNJ661 Man page
objective function Man page
Objective function Man page
out-degree Man page
parallel multi-core simulation Man page
PERTURBATION_analysis Man page
phenotypic phase plane analysis Man page
PHPP Man page
ramp-down Man page
ramp-up Man page
robustness analysis Man page
Robustness analysis using FVA Man page
S_aureus_iSB619 Man page
SBML Man page
S_cerevisiae_IND750 Man page
Search-metabolite Man page
SEARCH_metabolite Man page
Search-reaction Man page
SEARCH_reaction Man page
SINGLE_DEL_FLUXOME Man page
single knockouts Man page
solve FBA problem Man page
Sybil_2_FBA_obj Man page
Sybil_S4_object Man page
View_objective Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.