Index

A

add_cycle() (CNOGraph method) add_edge() (CNOGraph method) add_edges_from() (CNOGraph method) add_experiment() (MIDASBuilder method) (XMIDAS method) add_gaussian_noise() (XMIDAS method) add_list_experiments() (MIDASBuilder method) add_net() (NET method) add_node() (CNOGraph method) add_nodes_from() (CNOGraph method) add_path() (CNOGraph method) add_reaction() (CNOGraph method) (Interactions method) (Reactions method) (SIF method)

add_single_experiments() (Experiments method) add_star() (CNOGraph method) add_uniform_distributed_noise() (XMIDAS method) add_weighted_edges_from() (CNOGraph method) addMIDAS() (MultiMIDAS method) ADJ2SIF (class in cellnopt.core.adj2sif) adjacencyMatrix() (CNOGraph method) andNodes (SIF attribute) attributes (CNOGraph attribute) average_replicates() (XMIDAS method)

B

boxplot() (XMIDAS method)

C

CASPOModels (class in cellnopt.core.asp) cellLine (Experiment attribute) (XMIDAS attribute) cellLines (MultiMIDAS attribute) (XMIDAS attribute) cellnopt.core.adj2sif (module) cellnopt.core.asp (module) cellnopt.core.cnograph (module) cellnopt.core.converter (module) cellnopt.core.io.eda (module) cellnopt.core.io.kinexus (module) cellnopt.core.metabolites (module) cellnopt.core.midas (module) cellnopt.core.normalisation (module) cellnopt.core.reactions (module) cellnopt.core.sif (module) cellnopt.core.sif2asp (module) cellnopt.core.sop2sif (module) centrality_betweeness() (CNOGraph method) centrality_closeness() (CNOGraph method) centrality_degree() (CNOGraph method) centrality_eigenvector() (CNOGraph method)

clean_orphan_ands() (CNOGraph method) clear() (CNOGraph method) (SIF method) CNOGraph (class in cellnopt.core.cnograph) CNOGraphAttributes (class in cellnopt.core.cnograph) CNOGraphMultiEdges (class in cellnopt.core.cnograph) collapse_node() (CNOGraph method) collapse_nodes() (CNOGraph method) columns (Kinexus attribute) compress() (CNOGraph method) compressable_nodes (CNOGraph attribute) (CNOGraphMultiEdges attribute) constant() (TypicalTimeSeries method) control_normalisation() (XMIDASNormalise method) copy() (XMIDAS method) corr() (XMIDAS method) correlation_experiment_one_signal() (XMIDAS method) create_empty_simulation() (XMIDAS method) create_random_simulation() (XMIDAS method) cues_as_dict() (Experiment method) cutnonc() (CNOGraph method)

D

data (Experiment attribute) (Kinexus attribute) (SIF attribute) degree_histogram() (CNOGraph method) dependencyMatrix() (CNOGraph method) difference() (CNOGraph method) discretise() (XMIDAS method)

discretize() (XMIDAS method) dot_mode (CNOGraph attribute) draw() (CNOGraph method) dynamicRange() (NormaliseMIDAS method)

E

earlier() (TypicalTimeSeries method) EDA (class in cellnopt.core.io.eda) edges (SIF attribute) excludeInLogical (Reactions attribute) expand_and_gates() (CNOGraph method) expand_or_gates() (CNOGraph method) Experiment (class in cellnopt.core.midas)

Experiments (class in cellnopt.core.midas) experiments (XMIDAS attribute) export2experiments() (XMIDAS method) export2gexf() (CNOGraph method) export2midas() (Kinexus method) (MIDASBuilder method) export2SBMLQual() (CNOGraph method) (SIF method) export2sif() (ADJ2SIF method) (CASPOModels method) (CNOGraph method) (EDA method) (SOP2SIF method)

F

findnonc() (CNOGraph method)

G

G (ADJ2SIF attribute) get_average_model() (CASPOModels method) get_bestfit() (TypicalTimeSeries method) get_bestfit_color() (TypicalTimeSeries method) get_colnames() (MIDASBuilder method) get_control_name() (XMIDASNormalise method) get_cues() (Experiment method) get_diff() (XMIDAS method)

get_experiments_with_same_control() (XMIDASNormalise method) get_max_rank() (CNOGraph method) get_name_from_uniprot() (Kinexus method) get_node_attributes() (CNOGraph method) get_residual_errors() (XMIDAS method) get_same_rank() (CNOGraph method) get_share_file() (in module cellnopt.core)

H

hcluster() (CNOGraph method) (XMIDAS method) header_uniprot (Kinexus attribute)

heatmap() (XMIDAS method)

I

importSBMLQual() (SIF method) incTruthTable (Reactions attribute) index (Kinexus attribute) inhibitors (CNOGraph attribute) (Experiment attribute) (XMIDAS attribute)

Interactions (class in cellnopt.core.converter) intersect() (CNOGraph method) inverse_sustained() (TypicalTimeSeries method) is_compressable() (CNOGraph method) (CNOGraphMultiEdges method)

K

keys() (CNOGraphAttributes method)

Kinexus (class in cellnopt.core.io.kinexus)

L

later() (TypicalTimeSeries method) load_adjacency() (ADJ2SIF method) load_names() (ADJ2SIF method)

loadSIF() (SIF method) lookfor() (CNOGraph method)

M

mapping (SOP2SIF attribute) merge_nodes() (CNOGraph method) merge_times() (XMIDAS method) Metabolites (class in cellnopt.core.metabolites)

midas (CNOGraph attribute) MIDASBuilder (class in cellnopt.core.midas) monotony (Reactions attribute) MultiMIDAS (class in cellnopt.core.midas)

N

name (Reaction attribute) names (ADJ2SIF attribute) names_cues (XMIDAS attribute) names_inhibitors (XMIDAS attribute) names_signals (XMIDAS attribute) names_species (XMIDAS attribute) names_stimuli (XMIDAS attribute) namesSpecies (CNOGraph attribute) (Interactions attribute) (Reactions attribute) (SIF attribute) NET (class in cellnopt.core.asp) net (NET attribute)

net2reaction() (in module cellnopt.core.asp) nExps (XMIDAS attribute) nodes1 (SIF attribute) nodes2 (SIF attribute) nonc (CNOGraph attribute) normalise() (XMIDAS method) NormaliseMIDAS (class in cellnopt.core.normalisation) notedge() (SIF method) nSignals (XMIDAS attribute)

P

pca() (XMIDAS method) plot() (CNOGraph method) (MultiMIDAS method) (SIF method) (TypicalTimeSeries method) (XMIDAS method) plotdot() (CASPOModels method) (CNOGraph method) plotExp() (XMIDAS method)

plotMSEs() (XMIDAS method) plotSim() (XMIDAS method) preprocessing() (CNOGraph method) protein_name (Experiment attribute)

R

radviz() (XMIDAS method) random_poisson_graph() (CNOGraph method) reacBoxes (Reactions attribute) reacID (CNOGraph attribute) (Interactions attribute) (Reactions attribute) (SIF attribute) reacText (Reactions attribute) Reaction (class in cellnopt.core.converter) Reactions (class in cellnopt.core.reactions) read_csv() (Kinexus method) read_excel() (Kinexus method) readMIDAS() (MultiMIDAS method) readSIF() (CNOGraph method) recursive_compress() (CNOGraph method) relabel_nodes() (CNOGraph method) remove_and_gates() (CNOGraph method) (SIF method) remove_cellLine() (XMIDAS method) remove_edge() (CNOGraph method) (CNOGraphMultiEdges method) remove_edges_from() (CNOGraph method) remove_experiments() (XMIDAS method)

remove_inhibitors() (XMIDAS method) remove_node() (CNOGraph method) remove_nodes_from() (CNOGraph method) remove_reaction() (Interactions method) (Reactions method) (SIF method) remove_self_loops() (CNOGraph method) remove_species() (Interactions method) (Reactions method) (SIF method) (XMIDAS method) remove_stimuli() (XMIDAS method) remove_times() (XMIDAS method) rename_cellLine() (XMIDAS method) rename_inhibitors() (XMIDAS method) rename_node() (CNOGraph method) rename_species() (Reaction method) (XMIDAS method) rename_stimuli() (XMIDAS method) rename_time() (XMIDAS method) reset() (XMIDAS method) reset_edge_attributes() (CNOGraph method) (CNOGraphMultiEdges method) reset_index() (XMIDAS method) round() (XMIDAS method)

S

save() (SIF method) save2midas() (XMIDAS method) scale_max() (XMIDAS method) scale_max_across_experiments() (XMIDAS method) scale_max_by_experiments() (XMIDAS method) scale_min_max() (XMIDAS method) scale_min_max_across_experiments() (XMIDAS method) scale_min_max_by_experiments() (XMIDAS method) search() (Interactions method) (Reactions method) (SIF method) select_globally_normalised() (Kinexus method) set_default_edge_attributes() (CNOGraph method) set_default_node_attributes() (CNOGraph method) set_index() (XMIDAS method) set_random_experiments() (MIDASBuilder method) shuffle() (XMIDAS method) SIF (class in cellnopt.core.sif) sif() (CNOGraph method) SIF2ASP (class in cellnopt.core.sif2asp) sif2json() (SIF method)

sif2reaction() (SIF method) signals (CNOGraph attribute) (XMIDAS attribute) signs (SIF2ASP attribute) SOP2SIF (class in cellnopt.core.sop2sif) sop2sif() (SOP2SIF method) sort_experiments_by_inhibitors() (XMIDAS method) sort_experiments_by_stimuli() (XMIDAS method) specBoxes (Metabolites attribute) specDefault (Metabolites attribute) specID (Interactions attribute) (Metabolites attribute) (Reactions attribute) (SIF attribute) species (Experiments attribute) (XMIDAS attribute) specLongNames (Metabolites attribute) specNotes (Metabolites attribute) split_node() (CNOGraph method) stimuli (CNOGraph attribute) (Experiment attribute) (XMIDAS attribute) summary() (CNOGraph method) sustained() (TypicalTimeSeries method) swap_edges() (CNOGraph method)

T

test_example() (MIDASBuilder method) time (Experiment attribute) time_normalisation() (NormaliseMIDAS method) (XMIDASNormalise method) timeNormalisation() (NormaliseMIDAS method) times (TypicalTimeSeries attribute) (XMIDAS attribute)

timeScale (Reactions attribute) to_directed() (CNOGraph method) transient() (TypicalTimeSeries method) TypicalTimeSeries (class in cellnopt.core.midas)

U

union() (CNOGraph method)

units (Experiment attribute)

V

valid_symbols (Interactions attribute) (Reaction attribute) (Reactions attribute) (SIF attribute)

W

write2net() (SIF2ASP method) write2sif() (NET method) (Reactions method)

writeSIF() (Reactions method)

X

XMIDAS (class in cellnopt.core.midas) xmidas (MIDASBuilder attribute)

XMIDASNormalise (class in cellnopt.core.normalisation) xplot() (XMIDAS method)