Index

A

analyse_and_save_fluxes() (in module gsmm.csm.analyse_csm)

assign_reaction_confidences() (in module gsmm.csm.build_csm)

C

collect_sink_fluxes() (in module gsmm.csm.analyse_csm)

E

extract_fluxes() (in module gsmm.csm.analyse_csm)

extract_genes() (in module gsmm.csm.build_csm)

F

filter_and_save_results() (in module gsmm.csm.visualisation) filter_deletion_results() (in module gsmm.csm.analyse_csm)

filter_model_by_genes() (in module gsmm.csm.build_csm) filter_non_zero_fluxes() (in module gsmm.csm.analyse_csm) find_common_reactions() (in module gsmm.csm.analyse_csm)

G

get_sink_fluxes() (in module gsmm.csm.analyse_csm) gsmm module gsmm.csm module gsmm.csm.analyse_csm module

gsmm.csm.build_csm module gsmm.csm.config module gsmm.csm.visualisation module

L

load_data() (in module gsmm.csm.visualisation)

load_expression_data() (in module gsmm.csm.build_csm) load_models() (in module gsmm.csm.analyse_csm)

M

main() (in module gsmm.csm.build_csm) module gsmm gsmm.csm gsmm.csm.analyse_csm gsmm.csm.build_csm gsmm.csm.config gsmm.csm.visualisation

N

normalize_expression_data() (in module gsmm.csm.build_csm)

O

optimize_and_get_fluxes() (in module gsmm.csm.analyse_csm)

optimize_model() (in module gsmm.csm.build_csm)

P

perform_single_reaction_deletion() (in module gsmm.csm.analyse_csm) plot_flux_correlation_heatmap() (in module gsmm.csm.visualisation) plot_flux_distribution_clustermap() (in module gsmm.csm.visualisation)

plot_fluxes() (in module gsmm.csm.visualisation) plot_sink_flux_correlation_heatmap() (in module gsmm.csm.visualisation) plot_sink_fluxes_heatmap() (in module gsmm.csm.visualisation)

R

read_parent_model() (in module gsmm.csm.build_csm)

run_model_reconstruction() (in module gsmm.csm.build_csm)

S

save_data_for_visualization() (in module gsmm.csm.analyse_csm) save_filtered_reaction_deletion_results() (in module gsmm.csm.analyse_csm)

save_reaction_deletion_results() (in module gsmm.csm.analyse_csm) set_glpk_solver() (in module gsmm.csm.build_csm)