Index

A

AdjustedScoreIntegrationStrategy (class in troppo.omics.integration) annotations (troppo.tasks.core.Task property)

apply_evaluate() (troppo.tasks.core.Task method) apply_thresholding_filter() (troppo.omics.gene_level_thresholding.GeneLevelThresholding method)

B

batch_evaluate() (troppo.tasks.core.TaskEvaluator method) batch_function() (troppo.tasks.core.TaskEvaluator static method)

block_reactions_from_idxs() (troppo.methods.reconstruction.corda.CORDA method) build_final_model() (troppo.methods.gapfill.consensus.CombinatorialGapfill method) build_problem() (troppo.methods.reconstruction.tINIT.tINIT method)

C

check_if_blocked() (troppo.methods.reconstruction.corda.CORDA method) column_names (troppo.omics.core.TabularContainer property) combinatorial_gapfill() (troppo.methods.gapfill.pathway_analysis.CombinatorialEFMGapfill method) CombinatorialEFMGapfill (class in troppo.methods.gapfill.pathway_analysis) CombinatorialGapfill (class in troppo.methods.gapfill.consensus) combine() (troppo.tasks.core.Task method) combine_inplace() (troppo.tasks.core.Task method) CONSTRAINBY_PERC (troppo.methods.reconstruction.corda.CORDAProperties attribute) CONSTRAINBY_VAL (troppo.methods.reconstruction.corda.CORDAProperties attribute) ContextSpecificModelReconstructionAlgorithm (class in troppo.methods.base) ContextSpecificModelSimulator (class in troppo.validation.core)

ContinuousScoreIntegrationStrategy (class in troppo.omics.integration) convert_feature_ids() (troppo.omics.core.TypedOmicsMeasurementSet method) convertIds() (troppo.omics.core.OmicsContainer method) convertValues() (troppo.omics.core.OmicsContainer method) CORDA (class in troppo.methods.reconstruction.corda) CORDAProperties (class in troppo.methods.reconstruction.corda) CORSOModel (class in troppo.methods.reconstruction.corda) CORSOSolution (class in troppo.methods.reconstruction.corda) costfx_factory() (troppo.methods.reconstruction.corda.CORDA static method) current_task (troppo.tasks.core.TaskEvaluator property) CustomSelectionIntegrationStrategy (class in troppo.omics.integration)

D

data (troppo.omics.core.TabularContainer property) decode_mt_list() (in module troppo.methods.base) decode_rx_list() (in module troppo.methods.base) decoder_function (troppo.methods.base.GapfillProperties attribute)

default_post_processing_func() (in module troppo.validation.core) DefaultCoreIntegrationStrategy (class in troppo.omics.integration) do_function_for_reactions_on_both_models() (troppo.methods.reconstruction.corda.CORDA method) drop() (troppo.omics.core.TabularContainer method) dropNA() (troppo.omics.core.OmicsContainer method)

E

EFMGapfill (class in troppo.methods.gapfill.efm) EFMGapfillProperties (class in troppo.methods.gapfill.efm) empty_matrix() (troppo.methods.reconstruction.imat.IMAT static method)

evaluate() (troppo.tasks.core.TaskEvaluator method) evaluate_solution() (troppo.tasks.core.Task method) ExcelTaskIO (class in troppo.tasks.task_io)

F

FastCC (class in troppo.methods.gapfill.fastcc) fastcc() (troppo.methods.gapfill.fastcc.FastCC method) FastCCProperties (class in troppo.methods.gapfill.fastcc) FASTcore (class in troppo.methods.reconstruction.fastcore) fastcore() (troppo.methods.reconstruction.fastcore.FASTcore method) FastcoreProperties (class in troppo.methods.reconstruction.fastcore) filterById() (troppo.omics.core.OmicsContainer method) filterByValue() (troppo.omics.core.OmicsContainer method) find_core() (in module troppo.methods.reconstruction.swiftcore) find_dependent_reactions() (troppo.methods.reconstruction.corda.CORDA method)

find_reaction_limits() (troppo.methods.reconstruction.corda.CORDA method) findSparseMode() (troppo.methods.reconstruction.fastcore.FASTcore method) flux_constraints (troppo.tasks.core.Task property) from_integrated_scores() (troppo.methods.base.PropertiesReconstruction static method) (troppo.methods.reconstruction.corda.CORDAProperties static method) (troppo.methods.reconstruction.fastcore.FastcoreProperties static method) (troppo.methods.reconstruction.gimme.GIMMEProperties static method) (troppo.methods.reconstruction.imat.IMATProperties static method) (troppo.methods.reconstruction.swiftcore.SwiftcoreProperties static method) (troppo.methods.reconstruction.tINIT.tINITProperties static method)

G

gapfill() (troppo.methods.gapfill.consensus.CombinatorialGapfill method) (troppo.methods.gapfill.efm.EFMGapfill method) (troppo.methods.gapfill.pathway_analysis.SubEFMGapfill method) gapfill_partial_pair() (troppo.methods.gapfill.pathway_analysis.CombinatorialEFMGapfill method) GapfillAlgorithm (class in troppo.methods.base) GapfillProperties (class in troppo.methods.base) GeneLevelThresholding (class in troppo.omics.gene_level_thresholding) generate_imat_problem() (troppo.methods.reconstruction.imat.IMAT method) generate_LP3_problem() (troppo.methods.reconstruction.fastcore.FASTcore method) generate_partial_models() (troppo.methods.gapfill.consensus.CombinatorialGapfill static method) (troppo.methods.gapfill.pathway_analysis.CombinatorialEFMGapfill method) GenericReader (class in troppo.omics.readers.generic) get_add_reaction_args() (troppo.tasks.core.Task method) get_add_reaction_cmds() (troppo.tasks.core.Task method)

get_Condition() (troppo.omics.core.OmicsContainer method) get_Data() (troppo.omics.core.OmicsContainer method) get_enumerator() (troppo.methods.gapfill.efm.EFMGapfill method) get_id_table() (troppo.omics.core.IdentifierMapping method) get_integrated_data_map() (troppo.omics.core.OmicsContainer method) get_Nomenclature() (troppo.omics.core.OmicsContainer method) get_OmicsType() (troppo.omics.core.OmicsContainer method) get_reaction_activity() (troppo.methods.reconstruction.gimme.GIMMESolution method) get_scores() (troppo.omics.core.OmicsDataMap method) get_task_bounds() (troppo.tasks.core.Task method) GIMME (class in troppo.methods.reconstruction.gimme) GIMMEModel (class in troppo.methods.reconstruction.gimme) GIMMEProperties (class in troppo.methods.reconstruction.gimme) GIMMESolution (class in troppo.methods.reconstruction.gimme) global_thresholding() (troppo.omics.gene_level_thresholding.GeneLevelThresholding static method)

H

has_valid_dims() (in module troppo.omics.core)

HpaReader (class in troppo.omics.readers.hpa)

I

id_replace() (troppo.tasks.core.Task method) idConverter() (in module troppo.omics.id_converter) IdentifierMapping (class in troppo.omics.core) if_none_return_list() (in module troppo.utilities.list) IMAT (class in troppo.methods.reconstruction.imat) IMATProperties (class in troppo.methods.reconstruction.imat) inflow_dict (troppo.tasks.core.Task property) integrate() (troppo.omics.integration.AdjustedScoreIntegrationStrategy method) (troppo.omics.integration.ContinuousScoreIntegrationStrategy method) (troppo.omics.integration.CustomSelectionIntegrationStrategy method) (troppo.omics.integration.DefaultCoreIntegrationStrategy method) (troppo.omics.integration.ScoreIntegrationStrategy static method) (troppo.omics.integration.ThresholdSelectionIntegrationStrategy method)

involved_reactions (troppo.tasks.core.Task property) is_list() (in module troppo.utilities.list) is_list_else_empty() (in module troppo.utilities.list) is_valid_model() (troppo.methods.gapfill.consensus.CombinatorialGapfill method)

J

JSONTaskIO (class in troppo.tasks.task_io)

L

load() (troppo.omics.core.OmicsContainer method) (troppo.omics.readers.generic.GenericReader method) (troppo.omics.readers.hpa.HpaReader method) (troppo.omics.readers.microarray.ProbeReader method)

local_t1_thresholding() (troppo.omics.gene_level_thresholding.GeneLevelThresholding static method) local_t2_thresholding() (troppo.omics.gene_level_thresholding.GeneLevelThresholding static method) LP3() (troppo.methods.reconstruction.fastcore.FASTcore method) LP7() (troppo.methods.reconstruction.fastcore.FASTcore method) LP9() (troppo.methods.reconstruction.fastcore.FASTcore method)

M

mandatory_activity (troppo.tasks.core.Task property) map_ids() (troppo.omics.core.IdentifierMapping method) mapType() (troppo.omics.core.OmicsDataMap method) module troppo.methods.base troppo.methods.gapfill.consensus troppo.methods.gapfill.efm troppo.methods.gapfill.fastcc troppo.methods.gapfill.pathway_analysis troppo.methods.reconstruction.corda troppo.methods.reconstruction.fastcore troppo.methods.reconstruction.gimme troppo.methods.reconstruction.imat troppo.methods.reconstruction.swiftcore troppo.methods.reconstruction.tINIT troppo.omics.core troppo.omics.gene_level_thresholding troppo.omics.id_converter troppo.omics.integration troppo.omics.readers.generic troppo.omics.readers.hpa troppo.omics.readers.microarray troppo.tasks.core troppo.tasks.task_io troppo.utilities.list troppo.utilities.statistics troppo.validation.core

N

name (troppo.omics.core.IdentifierMapping property) (troppo.tasks.core.Task property)

normalize() (in module troppo.utilities.statistics)

O

omics_type (troppo.omics.core.TypedOmicsMeasurementSet property) OmicsContainer (class in troppo.omics.core) OmicsDataMap (class in troppo.omics.core)

OmicsMeasurementSet (class in troppo.omics.core) optimize_corso() (troppo.methods.reconstruction.corda.CORSOModel method) optimize_gimme() (troppo.methods.reconstruction.gimme.GIMMEModel method) outflow_dict (troppo.tasks.core.Task property)

P

prepocessing() (troppo.methods.gapfill.fastcc.FastCC method) preprocessing() (troppo.methods.reconstruction.fastcore.FASTcore method) (troppo.methods.reconstruction.tINIT.tINIT method) print_values() (troppo.omics.core.OmicsContainer method) ProbeReader (class in troppo.omics.readers.microarray) properties_class (troppo.methods.base.ContextSpecificModelReconstructionAlgorithm property) (troppo.methods.base.GapfillAlgorithm property) (troppo.methods.gapfill.efm.EFMGapfill attribute) (troppo.methods.reconstruction.corda.CORDA attribute) (troppo.methods.reconstruction.fastcore.FASTcore attribute) (troppo.methods.reconstruction.gimme.GIMME attribute) (troppo.methods.reconstruction.imat.IMAT attribute) (troppo.methods.reconstruction.swiftcore.SWIFTCORE attribute) (troppo.methods.reconstruction.tINIT.tINIT attribute)

PropertiesReconstruction (class in troppo.methods.base) prune_model() (troppo.methods.gapfill.pathway_analysis.CombinatorialEFMGapfill method)

R

reaction_dict (troppo.tasks.core.Task property) ReactionProtectionMixin (class in troppo.omics.integration) read_from_string() (troppo.tasks.task_io.ExcelTaskIO method) (troppo.tasks.task_io.JSONTaskIO method) (troppo.tasks.task_io.TaskIO method) read_task() (troppo.tasks.task_io.ExcelTaskIO method) (troppo.tasks.task_io.TaskIO method) reverse_irreversible_reactions_in_reverse_direction() (troppo.methods.reconstruction.fastcore.FASTcore method) row_names (troppo.omics.core.TabularContainer property) run() (troppo.methods.base.ContextSpecificModelReconstructionAlgorithm method) (troppo.methods.base.GapfillAlgorithm method) (troppo.methods.gapfill.efm.EFMGapfill method) (troppo.methods.gapfill.fastcc.FastCC method) (troppo.methods.reconstruction.corda.CORDA method) (troppo.methods.reconstruction.fastcore.FASTcore method) (troppo.methods.reconstruction.gimme.GIMME method) (troppo.methods.reconstruction.imat.IMAT method) (troppo.methods.reconstruction.swiftcore.SWIFTCORE method) (troppo.methods.reconstruction.tINIT.tINIT method)

run_corda() (troppo.methods.reconstruction.corda.CORDA method) run_imat() (troppo.methods.reconstruction.imat.IMAT method) run_tINIT() (troppo.methods.reconstruction.tINIT.tINIT method)

S

ScoreIntegrationStrategy (class in troppo.omics.integration) searchNomenclature() (in module troppo.omics.id_converter) select() (troppo.omics.core.OmicsDataMap method) set_condition() (troppo.omics.core.OmicsContainer method) set_corso_objective() (troppo.methods.reconstruction.corda.CORSOModel method) set_costs() (troppo.methods.reconstruction.corda.CORSOModel method) set_data() (troppo.omics.core.OmicsContainer method) set_scores() (troppo.omics.core.OmicsDataMap method)

set_type() (troppo.omics.core.OmicsContainer method) should_fail (troppo.tasks.core.Task property) simulate() (troppo.validation.core.ContextSpecificModelSimulator method) simulate_context() (in module troppo.methods.gapfill.pathway_analysis) solve_original_model() (troppo.methods.reconstruction.corda.CORSOModel method) solve_problem() (troppo.methods.reconstruction.tINIT.tINIT method) SubEFMGapfill (class in troppo.methods.gapfill.pathway_analysis) SWIFTCORE (class in troppo.methods.reconstruction.swiftcore) SwiftcoreProperties (class in troppo.methods.reconstruction.swiftcore)

T

TabularContainer (class in troppo.omics.core) TabularReader (class in troppo.omics.readers.generic) Task (class in troppo.tasks.core) TaskEvaluator (class in troppo.tasks.core) TaskIO (class in troppo.tasks.task_io) tasks (troppo.tasks.core.TaskEvaluator property) threshold_strategy() (troppo.omics.gene_level_thresholding.GeneLevelThresholding method) ThresholdSelectionIntegrationStrategy (class in troppo.omics.integration) tINIT (class in troppo.methods.reconstruction.tINIT) tINITProperties (class in troppo.methods.reconstruction.tINIT) to_containers() (troppo.omics.readers.generic.TabularReader method) to_omics_container() (troppo.omics.core.OmicsMeasurementSet method) (troppo.omics.core.TypedOmicsMeasurementSet method) transform() (troppo.omics.core.OmicsContainer method) (troppo.omics.core.TabularContainer method) troppo.methods.base module troppo.methods.gapfill.consensus module troppo.methods.gapfill.efm module troppo.methods.gapfill.fastcc module troppo.methods.gapfill.pathway_analysis module troppo.methods.reconstruction.corda module troppo.methods.reconstruction.fastcore module troppo.methods.reconstruction.gimme module

troppo.methods.reconstruction.imat module troppo.methods.reconstruction.swiftcore module troppo.methods.reconstruction.tINIT module troppo.omics.core module troppo.omics.gene_level_thresholding module troppo.omics.id_converter module troppo.omics.integration module troppo.omics.readers.generic module troppo.omics.readers.hpa module troppo.omics.readers.microarray module troppo.tasks.core module troppo.tasks.task_io module troppo.utilities.list module troppo.utilities.statistics module troppo.validation.core module TypedOmicsMeasurementSet (class in troppo.omics.core)

W

write_task() (troppo.tasks.task_io.TaskIO method) write_to_string() (troppo.tasks.task_io.ExcelTaskIO method) (troppo.tasks.task_io.JSONTaskIO method) (troppo.tasks.task_io.TaskIO method)

Z

z_score() (in module troppo.utilities.statistics)