Index

_

_ColorGenerator__generate_intervals() (NetExplorer.models.colors.ColorGenerator method) _ColorGenerator__normalize() (NetExplorer.models.colors.ColorGenerator method) _Condition__get_max_expression() (NetExplorer.models.mysql_models.Condition method) _GeneOntology__query_go() (NetExplorer.models.neo4j_models.GeneOntology method) _get_contig_data() (NetExplorer.models.downloaders.DownloadHandler method) _get_go_data() (NetExplorer.models.downloaders.DownloadHandler method) _get_homology_data() (NetExplorer.models.downloaders.DownloadHandler method) _get_interactions_data() (NetExplorer.models.downloaders.DownloadHandler method) _get_orf_data() (NetExplorer.models.downloaders.DownloadHandler method) _get_pfam_data() (NetExplorer.models.downloaders.DownloadHandler method) _Node__query_node() (NetExplorer.models.neo4j_models.Node method)

_oldExperiment__get_minmax() (NetExplorer.models.neo4j_models.oldExperiment method) _PlanarianContig__query_node() (NetExplorer.models.neo4j_models.PlanarianContig method) _PlanarianGene__query_node() (NetExplorer.models.neo4j_models.PlanarianGene method) _PlotCreator__create_bar() (NetExplorer.models.plots.PlotCreator method) _PlotCreator__create_coexpression() (NetExplorer.models.plots.PlotCreator method) _PlotCreator__create_heatmap() (NetExplorer.models.plots.PlotCreator method) _PlotCreator__create_linechart() (NetExplorer.models.plots.PlotCreator method) _PlotCreator__create_tsne() (NetExplorer.models.plots.PlotCreator method) _PlotCreator__create_tsne_multiple() (NetExplorer.models.plots.PlotCreator method) _PlotCreator__create_tsne_simple() (NetExplorer.models.plots.PlotCreator method) _PlotCreator__create_violin() (NetExplorer.models.plots.PlotCreator method) _PredInteraction__query_interaction() (NetExplorer.models.neo4j_models.PredInteraction method)

A

about() (in module NetExplorer.views.pages.about) accession (NetExplorer.models.neo4j_models.Domain attribute) (NetExplorer.models.neo4j_models.GeneOntology attribute) account() (in module NetExplorer.views.pages.account) add_color_to_trace() (NetExplorer.models.plots.VolcanoPlot method) add_conditions() (NetExplorer.models.plots.HeatmapPlot method) add_elements() (NetExplorer.models.downloaders.ServedFile method) (NetExplorer.models.neo4j_models.GraphCytoscape method) add_gene() (NetExplorer.models.plots.HeatmapPlot method) add_gene_expression() (NetExplorer.models.plots.HeatmapPlot method) add_graph() (NetExplorer.models.neo4j_models.GraphCytoscape method) add_interaction() (NetExplorer.models.neo4j_models.GraphCytoscape method)

add_name() (NetExplorer.models.plots.VolcanoPlot method) add_node() (NetExplorer.models.neo4j_models.GraphCytoscape method) add_trace() (NetExplorer.models.plots.VolcanoPlot method) add_units() (NetExplorer.models.plots.VolcanoPlot method) add_x() (NetExplorer.models.plots.VolcanoPlot method) add_y() (NetExplorer.models.plots.VolcanoPlot method) allowed_databases (NetExplorer.models.neo4j_models.HumanNode attribute) (NetExplorer.models.neo4j_models.Node attribute) (NetExplorer.models.neo4j_models.PlanarianContig attribute), [1] (NetExplorer.models.neo4j_models.PlanarianGene attribute) auc (NetExplorer.models.mysql_models.ClusterMarkers attribute), [1] autocomplete() (in module NetExplorer.views.http_api.plannet.autocomplete) avg_diff (NetExplorer.models.mysql_models.ClusterMarkers attribute), [1]

B

BarPlot (class in NetExplorer.models.plots) blast() (in module NetExplorer.views.pages.blast) blast_brh (NetExplorer.models.neo4j_models.Homology attribute) blast_cov (NetExplorer.models.neo4j_models.Homology attribute)

blast_eval (NetExplorer.models.neo4j_models.Homology attribute) blue (NetExplorer.models.colors.ColorProfiles attribute) blue_red (NetExplorer.models.colors.ColorProfiles attribute) blue_white (NetExplorer.models.colors.ColorProfiles attribute)

C

cell_type (NetExplorer.models.mysql_models.Condition attribute), [1] CellPlotPosition (class in NetExplorer.models.mysql_models) CellPlotPosition.DoesNotExist CellPlotPosition.MultipleObjectsReturned cellplotposition_set (NetExplorer.models.mysql_models.Dataset attribute) (NetExplorer.models.mysql_models.Experiment attribute) (NetExplorer.models.mysql_models.Sample attribute) chromosome (NetExplorer.models.neo4j_models.PlanarianGene attribute) citation (NetExplorer.models.mysql_models.Dataset attribute), [1] (NetExplorer.models.mysql_models.Experiment attribute), [1] cluster_markers() (in module NetExplorer.views.http_api.planexp.general.cluster_markers) ClusterMarkers (class in NetExplorer.models.mysql_models) ClusterMarkers.DoesNotExist ClusterMarkers.MultipleObjectsReturned clustermarkers_set (NetExplorer.models.mysql_models.Condition attribute) (NetExplorer.models.mysql_models.Dataset attribute) (NetExplorer.models.mysql_models.Experiment attribute) cmax (NetExplorer.models.plots.ScatterPlot attribute) cmin (NetExplorer.models.plots.ScatterPlot attribute) color_gradient() (NetExplorer.models.neo4j_models.oldExperiment method) ColorGenerator (class in NetExplorer.models.colors) ColorProfiles (class in NetExplorer.models.colors) compute_color_limits() (NetExplorer.models.plots.ScatterPlot method) cond_type (NetExplorer.models.mysql_models.Condition attribute), [1] (NetExplorer.models.mysql_models.ExpressionRelative attribute), [1]

cond_type_id (NetExplorer.models.mysql_models.Condition attribute) (NetExplorer.models.mysql_models.ExpressionRelative attribute) Condition (class in NetExplorer.models.mysql_models) condition (NetExplorer.models.mysql_models.ClusterMarkers attribute), [1] (NetExplorer.models.mysql_models.ExpressionCondition attribute), [1] (NetExplorer.models.mysql_models.SampleCondition attribute), [1] Condition.DoesNotExist Condition.MultipleObjectsReturned condition1 (NetExplorer.models.mysql_models.ExpressionRelative attribute), [1] condition1_expressionrelative_set (NetExplorer.models.mysql_models.Condition attribute) condition1_expressionrelative_setsubcondition (NetExplorer.models.mysql_models.Condition attribute) condition1_id (NetExplorer.models.mysql_models.ExpressionRelative attribute) condition2 (NetExplorer.models.mysql_models.ExpressionRelative attribute), [1] condition2_id (NetExplorer.models.mysql_models.ExpressionRelative attribute) condition_id (NetExplorer.models.mysql_models.ClusterMarkers attribute) (NetExplorer.models.mysql_models.ExpressionCondition attribute) (NetExplorer.models.mysql_models.SampleCondition attribute) condition_set (NetExplorer.models.mysql_models.ConditionType attribute) (NetExplorer.models.mysql_models.Experiment attribute) condition_sort() (in module NetExplorer.views.helpers.common) ConditionType (class in NetExplorer.models.mysql_models) ConditionType.DoesNotExist ConditionType.MultipleObjectsReturned create_plot() (NetExplorer.models.plots.PlotCreator method)

D

data_from_node (NetExplorer.models.downloaders.DownloadHandler attribute) database (NetExplorer.models.neo4j_models.GeneSearch attribute) (NetExplorer.models.neo4j_models.KeggPathway attribute) (NetExplorer.models.neo4j_models.Node attribute) (NetExplorer.models.neo4j_models.PlanarianContig attribute) (NetExplorer.models.neo4j_models.PlanarianGene attribute) (NetExplorer.models.neo4j_models.PredInteraction attribute) (NetExplorer.models.neo4j_models.WildCard attribute) Dataset (class in NetExplorer.models.mysql_models) dataset (NetExplorer.models.mysql_models.CellPlotPosition attribute), [1] (NetExplorer.models.mysql_models.ClusterMarkers attribute), [1] (NetExplorer.models.mysql_models.ExperimentDataset attribute), [1] (NetExplorer.models.mysql_models.ExpressionAbsolute attribute), [1] (NetExplorer.models.mysql_models.ExpressionRelative attribute), [1] (NetExplorer.models.mysql_models.RegulatoryLinks attribute), [1] (NetExplorer.models.mysql_models.UserDatasetPermission attribute), [1] Dataset.DoesNotExist Dataset.MultipleObjectsReturned dataset_id (NetExplorer.models.mysql_models.CellPlotPosition attribute) (NetExplorer.models.mysql_models.ClusterMarkers attribute) (NetExplorer.models.mysql_models.ExperimentDataset attribute) (NetExplorer.models.mysql_models.ExpressionAbsolute attribute) (NetExplorer.models.mysql_models.ExpressionRelative attribute) (NetExplorer.models.mysql_models.RegulatoryLinks attribute) (NetExplorer.models.mysql_models.UserDatasetPermission attribute)

datasets (NetExplorer.models.neo4j_models.ExperimentList attribute) datasets() (in module NetExplorer.views.pages.datasets) define_important() (NetExplorer.models.neo4j_models.GraphCytoscape method) defines_cell_type (NetExplorer.models.mysql_models.Condition attribute), [1] degree (NetExplorer.models.neo4j_models.PlanarianContig attribute) description (NetExplorer.models.mysql_models.Condition attribute), [1] (NetExplorer.models.mysql_models.ConditionType attribute), [1] (NetExplorer.models.mysql_models.Experiment attribute), [1] (NetExplorer.models.mysql_models.ExperimentType attribute), [1] (NetExplorer.models.neo4j_models.Domain attribute) disambiguate_gene() (in module NetExplorer.views.helpers.common) do_volcano_plot() (in module NetExplorer.views.http_api.planexp.general.experiment_dge_table) docfile (NetExplorer.models.neo4j_models.Document attribute) Document (class in NetExplorer.models.neo4j_models) Document.DoesNotExist Document.MultipleObjectsReturned Domain (class in NetExplorer.models.neo4j_models) domain (NetExplorer.models.neo4j_models.GeneOntology attribute) (NetExplorer.models.neo4j_models.HasDomain attribute) domains (NetExplorer.models.neo4j_models.Node attribute) domains_to_json() (NetExplorer.models.neo4j_models.Node method) download_data() (NetExplorer.models.downloaders.DownloadHandler method) downloader() (in module NetExplorer.views.http_api.plannet.downloader) DownloadHandler (class in NetExplorer.models.downloaders) downloads() (in module NetExplorer.views.pages.downloads)

E

edges (NetExplorer.models.neo4j_models.GraphCytoscape attribute) elements (NetExplorer.models.downloaders.ServedFile attribute) end (NetExplorer.models.neo4j_models.PlanarianGene attribute) exp_type (NetExplorer.models.mysql_models.Experiment attribute), [1] (NetExplorer.models.mysql_models.ExperimentType attribute), [1] exp_type_id (NetExplorer.models.mysql_models.Experiment attribute) Experiment (class in NetExplorer.models.mysql_models) experiment (NetExplorer.models.mysql_models.CellPlotPosition attribute), [1] (NetExplorer.models.mysql_models.ClusterMarkers attribute), [1] (NetExplorer.models.mysql_models.Condition attribute), [1] (NetExplorer.models.mysql_models.ExperimentDataset attribute), [1] (NetExplorer.models.mysql_models.ExperimentGene attribute), [1] (NetExplorer.models.mysql_models.ExpressionAbsolute attribute), [1] (NetExplorer.models.mysql_models.ExpressionCondition attribute), [1] (NetExplorer.models.mysql_models.ExpressionRelative attribute), [1] (NetExplorer.models.mysql_models.RegulatoryLinks attribute), [1] (NetExplorer.models.mysql_models.Sample attribute), [1] (NetExplorer.models.mysql_models.SampleCondition attribute), [1] (NetExplorer.models.mysql_models.UserExperimentPermission attribute), [1] Experiment.DoesNotExist Experiment.MultipleObjectsReturned experiment_condition_types() (in module NetExplorer.views.http_api.planexp.general.experiment_condition_types) experiment_conditions() (in module NetExplorer.views.http_api.planexp.general.experiment_conditions) experiment_dataset() (in module NetExplorer.views.http_api.planexp.general.experiment_dataset) experiment_dge_table() (in module NetExplorer.views.http_api.planexp.general.experiment_dge_table) experiment_id (NetExplorer.models.mysql_models.CellPlotPosition attribute) (NetExplorer.models.mysql_models.ClusterMarkers attribute) (NetExplorer.models.mysql_models.Condition attribute) (NetExplorer.models.mysql_models.ExperimentDataset attribute) (NetExplorer.models.mysql_models.ExperimentGene attribute) (NetExplorer.models.mysql_models.ExpressionAbsolute attribute) (NetExplorer.models.mysql_models.ExpressionCondition attribute) (NetExplorer.models.mysql_models.ExpressionRelative attribute) (NetExplorer.models.mysql_models.RegulatoryLinks attribute) (NetExplorer.models.mysql_models.Sample attribute) (NetExplorer.models.mysql_models.SampleCondition attribute) (NetExplorer.models.mysql_models.UserExperimentPermission attribute)

experiment_set (NetExplorer.models.mysql_models.ExperimentType attribute) experiment_summary() (in module NetExplorer.views.http_api.planexp.general.experiment_summary) ExperimentDataset (class in NetExplorer.models.mysql_models) ExperimentDataset.DoesNotExist ExperimentDataset.MultipleObjectsReturned experimentdataset_set (NetExplorer.models.mysql_models.Dataset attribute) (NetExplorer.models.mysql_models.Experiment attribute) ExperimentGene (class in NetExplorer.models.mysql_models) ExperimentGene.DoesNotExist ExperimentGene.MultipleObjectsReturned experimentgene_set (NetExplorer.models.mysql_models.Experiment attribute) ExperimentList (class in NetExplorer.models.neo4j_models) experiments (NetExplorer.models.neo4j_models.ExperimentList attribute) ExperimentType (class in NetExplorer.models.mysql_models) ExperimentType.DoesNotExist ExperimentType.MultipleObjectsReturned expression_value (NetExplorer.models.mysql_models.ExpressionAbsolute attribute), [1] ExpressionAbsolute (class in NetExplorer.models.mysql_models) ExpressionAbsolute.DoesNotExist ExpressionAbsolute.MultipleObjectsReturned expressionabsolute_set (NetExplorer.models.mysql_models.Dataset attribute) (NetExplorer.models.mysql_models.Experiment attribute) (NetExplorer.models.mysql_models.Sample attribute) ExpressionCondition (class in NetExplorer.models.mysql_models) ExpressionCondition.DoesNotExist ExpressionCondition.MultipleObjectsReturned expressioncondition_set (NetExplorer.models.mysql_models.Condition attribute) (NetExplorer.models.mysql_models.Experiment attribute) ExpressionRelative (class in NetExplorer.models.mysql_models) ExpressionRelative.DoesNotExist ExpressionRelative.MultipleObjectsReturned expressionrelative_set (NetExplorer.models.mysql_models.ConditionType attribute) (NetExplorer.models.mysql_models.Dataset attribute) (NetExplorer.models.mysql_models.Experiment attribute)

F

fformat (NetExplorer.models.downloaders.ServedFile attribute) filename (NetExplorer.models.downloaders.ServedFile attribute)

filter() (NetExplorer.models.neo4j_models.GraphCytoscape method) filter_network() (in module NetExplorer.views.http_api.planexp.general.filter_network) fold_change (NetExplorer.models.mysql_models.ExpressionRelative attribute), [1]

G

gccount (NetExplorer.models.neo4j_models.PlanarianContig attribute) gene (NetExplorer.models.neo4j_models.PlanarianContig attribute) gene_ontologies (NetExplorer.models.neo4j_models.PlanarianContig attribute) gene_search() (in module NetExplorer.views.pages.gene_search) gene_symbol (NetExplorer.models.mysql_models.ClusterMarkers attribute), [1] (NetExplorer.models.mysql_models.ExperimentGene attribute), [1] (NetExplorer.models.mysql_models.ExpressionAbsolute attribute), [1] (NetExplorer.models.mysql_models.ExpressionCondition attribute), [1] (NetExplorer.models.mysql_models.ExpressionRelative attribute), [1] GeneExpPlot (class in NetExplorer.models.plots) GeneOntology (class in NetExplorer.models.neo4j_models) GeneOntologyEnrichment (class in NetExplorer.models.gene_ontology) GeneSearch (class in NetExplorer.models.neo4j_models) get_all_information() (NetExplorer.models.neo4j_models.PlanarianContig method) get_allowed_datasets() (NetExplorer.models.mysql_models.Dataset class method) get_allowed_experiments() (NetExplorer.models.mysql_models.Experiment class method) get_best_transcript() (NetExplorer.models.neo4j_models.PlanarianGene method) get_card() (in module NetExplorer.views.http_api.plannet.get_card) get_color() (NetExplorer.models.mysql_models.Condition method) get_color_legend() (NetExplorer.models.colors.ColorGenerator method) (NetExplorer.models.mysql_models.Condition method) get_condition_expression() (NetExplorer.models.mysql_models.ExpressionCondition class method) get_connections() (NetExplorer.models.neo4j_models.GraphCytoscape method) get_dataset_regexes() (in module NetExplorer.views.http_api.planexp.general.get_dataset_regexes) get_datasets() (NetExplorer.models.neo4j_models.ExperimentList method) get_domains() (NetExplorer.models.neo4j_models.Node method) get_enriched_gos() (NetExplorer.models.gene_ontology.GeneOntologyEnrichment method) get_expression() (NetExplorer.models.neo4j_models.GraphCytoscape method) (NetExplorer.models.neo4j_models.PlanarianContig method) get_fasta() (in module NetExplorer.views.http_api.plannet.get_fasta) get_filename() (NetExplorer.models.downloaders.DownloadHandler method) get_gene_name() (NetExplorer.models.neo4j_models.PlanarianContig method) get_geneontology() (NetExplorer.models.neo4j_models.PlanarianContig method) get_genes() (NetExplorer.models.neo4j_models.PlanarianContig method) get_genes_bulk() (NetExplorer.models.neo4j_models.GraphCytoscape class method) get_go_list() (NetExplorer.models.gene_ontology.GeneOntologyEnrichment method) get_goea() (in module NetExplorer.views.http_api.planexp.general.get_goea)

get_graph_from_kegg() (NetExplorer.models.neo4j_models.KeggPathway method) get_graphelements() (NetExplorer.models.neo4j_models.PlanarianContig method) get_header() (NetExplorer.models.downloaders.DownloadHandler method) get_homolog() (NetExplorer.models.neo4j_models.PlanarianContig method) (NetExplorer.models.neo4j_models.PlanarianGene method) get_homologs() (NetExplorer.models.neo4j_models.HumanNode method) get_homologs_bulk() (NetExplorer.models.neo4j_models.GraphCytoscape class method) get_human_genes() (NetExplorer.models.neo4j_models.GeneOntology method) (NetExplorer.models.neo4j_models.GeneSearch method) (NetExplorer.models.neo4j_models.WildCard method) get_mean_expression() (NetExplorer.models.mysql_models.ExpressionAbsolute class method) get_neighbours() (NetExplorer.models.neo4j_models.HumanNode method) (NetExplorer.models.neo4j_models.PlanarianContig method) get_neighbours_shallow() (NetExplorer.models.neo4j_models.PlanarianContig method) get_planarian_contigs() (NetExplorer.models.neo4j_models.Domain method) (NetExplorer.models.neo4j_models.GeneOntology method) (NetExplorer.models.neo4j_models.GeneSearch method) (NetExplorer.models.neo4j_models.HumanNode method) (NetExplorer.models.neo4j_models.PlanarianGene method) get_planarian_genes() (NetExplorer.models.neo4j_models.GeneSearch method) (NetExplorer.models.neo4j_models.HumanNode method) (NetExplorer.models.neo4j_models.WildCard method) get_plots() (NetExplorer.models.gene_ontology.GeneOntologyEnrichment method) get_possible_comparisons() (in module NetExplorer.views.http_api.planexp.general.experiment_conditions) get_sample_expression() (NetExplorer.models.mysql_models.ExpressionAbsolute class method) get_samples() (NetExplorer.models.neo4j_models.ExperimentList method) get_samples_per_condition() (NetExplorer.models.mysql_models.Condition class method) get_search_summary() (in module NetExplorer.views.pages.gene_search) get_shortest_paths() (in module NetExplorer.views.helpers.common) get_summary() (NetExplorer.models.neo4j_models.HumanNode method) (NetExplorer.models.neo4j_models.PlanarianContig method) go_regexp (NetExplorer.models.neo4j_models.GeneOntology attribute) goe (NetExplorer.models.gene_ontology.GeneOntologyEnrichment attribute) GraphCytoscape (class in NetExplorer.models.neo4j_models) graphelements (NetExplorer.models.neo4j_models.KeggPathway attribute) green (NetExplorer.models.colors.ColorProfiles attribute) group (NetExplorer.models.mysql_models.RegulatoryLinks attribute), [1]

H

handler404() (in module NetExplorer.views.http_api.plannet.error_handler) handler500() (in module NetExplorer.views.http_api.plannet.error_handler) HasDomain (class in NetExplorer.models.neo4j_models) header (NetExplorer.models.downloaders.ServedFile attribute) HeatmapPlot (class in NetExplorer.models.plots)

homolog (NetExplorer.models.neo4j_models.PlanarianContig attribute) (NetExplorer.models.neo4j_models.PlanarianGene attribute) Homology (class in NetExplorer.models.neo4j_models) human (NetExplorer.models.neo4j_models.Homology attribute) human_nodes (NetExplorer.models.neo4j_models.GeneOntology attribute) HumanNode (class in NetExplorer.models.neo4j_models)

I

id (NetExplorer.models.mysql_models.CellPlotPosition attribute) (NetExplorer.models.mysql_models.ClusterMarkers attribute) (NetExplorer.models.mysql_models.Condition attribute) (NetExplorer.models.mysql_models.ConditionType attribute) (NetExplorer.models.mysql_models.Dataset attribute) (NetExplorer.models.mysql_models.Experiment attribute) (NetExplorer.models.mysql_models.ExperimentDataset attribute) (NetExplorer.models.mysql_models.ExperimentGene attribute) (NetExplorer.models.mysql_models.ExperimentType attribute) (NetExplorer.models.mysql_models.ExpressionAbsolute attribute) (NetExplorer.models.mysql_models.ExpressionCondition attribute) (NetExplorer.models.mysql_models.ExpressionRelative attribute) (NetExplorer.models.mysql_models.RegulatoryLinks attribute) (NetExplorer.models.mysql_models.Sample attribute) (NetExplorer.models.mysql_models.SampleCondition attribute) (NetExplorer.models.mysql_models.UserDatasetPermission attribute) (NetExplorer.models.mysql_models.UserExperimentPermission attribute) (NetExplorer.models.neo4j_models.Document attribute) (NetExplorer.models.neo4j_models.oldExperiment attribute)

identifier (NetExplorer.models.neo4j_models.Domain attribute) identifier_regex (NetExplorer.models.mysql_models.Dataset attribute), [1] important (NetExplorer.models.neo4j_models.PlanarianContig attribute) index() (in module NetExplorer.views.pages.index) infer_symbol_database() (NetExplorer.models.neo4j_models.GeneSearch method) is_empty() (NetExplorer.models.neo4j_models.GraphCytoscape method) (NetExplorer.models.plots.GeneExpPlot method) (NetExplorer.models.plots.HeatmapPlot method) is_interaction (NetExplorer.models.mysql_models.ConditionType attribute), [1] is_one_sample() (NetExplorer.models.mysql_models.Experiment method) is_symbol_valid() (NetExplorer.models.mysql_models.Dataset method) (NetExplorer.models.neo4j_models.Domain class method) (NetExplorer.models.neo4j_models.GeneOntology class method) (NetExplorer.models.neo4j_models.PlanarianGene class method)

J

jitter_and_round() (NetExplorer.models.plots.ViolinPlot method)

K

kegg_url (NetExplorer.models.neo4j_models.KeggPathway attribute)

KeggPathway (class in NetExplorer.models.neo4j_models)

L

LinePlot (class in NetExplorer.models.plots)

M

map_color() (NetExplorer.models.colors.ColorGenerator method) map_expression() (in module NetExplorer.views.http_api.plannet.map_expression) map_expression_one() (in module NetExplorer.views.http_api.planexp.general.map_expression_one) map_expression_two() (in module NetExplorer.views.http_api.planexp.general.map_expression_two) max (NetExplorer.models.colors.ColorGenerator attribute)

max_expression (NetExplorer.models.mysql_models.Condition attribute), [1] maxexp (NetExplorer.models.neo4j_models.oldExperiment attribute) min (NetExplorer.models.colors.ColorGenerator attribute) min_expression (NetExplorer.models.mysql_models.Condition attribute), [1] minexp (NetExplorer.models.neo4j_models.oldExperiment attribute) mlength (NetExplorer.models.neo4j_models.Domain attribute)

N

n_contigs (NetExplorer.models.mysql_models.Dataset attribute), [1] n_ints (NetExplorer.models.mysql_models.Dataset attribute), [1] name (NetExplorer.models.mysql_models.Condition attribute), [1] (NetExplorer.models.mysql_models.ConditionType attribute), [1] (NetExplorer.models.mysql_models.Dataset attribute), [1] (NetExplorer.models.mysql_models.Experiment attribute), [1] (NetExplorer.models.neo4j_models.GeneOntology attribute) (NetExplorer.models.neo4j_models.PlanarianContig attribute) (NetExplorer.models.neo4j_models.PlanarianGene attribute) (NetExplorer.models.plots.PlotlyTrace attribute) neighbours (NetExplorer.models.neo4j_models.Node attribute) net_explorer() (in module NetExplorer.views.pages.net_explorer) NetExplorer.models.colors (module) NetExplorer.models.downloaders (module) NetExplorer.models.gene_ontology (module) NetExplorer.models.mysql_models (module) NetExplorer.models.neo4j_models (module) NetExplorer.models.neo4j_queries (module) NetExplorer.models.plots (module) NetExplorer.views.helpers.common (module) NetExplorer.views.http_api.planexp.general.cluster_markers (module) NetExplorer.views.http_api.planexp.general.experiment_condition_types (module) NetExplorer.views.http_api.planexp.general.experiment_conditions (module) NetExplorer.views.http_api.planexp.general.experiment_dataset (module) NetExplorer.views.http_api.planexp.general.experiment_dge_table (module) NetExplorer.views.http_api.planexp.general.experiment_summary (module) NetExplorer.views.http_api.planexp.general.filter_network (module) NetExplorer.views.http_api.planexp.general.get_dataset_regexes (module) NetExplorer.views.http_api.planexp.general.get_goea (module)

NetExplorer.views.http_api.planexp.general.map_expression_one (module) NetExplorer.views.http_api.planexp.general.map_expression_two (module) NetExplorer.views.http_api.planexp.general.regulatory_links (module) NetExplorer.views.http_api.planexp.plots.plot_gene_coexpression (module) NetExplorer.views.http_api.planexp.plots.plot_gene_expression (module) NetExplorer.views.http_api.planexp.plots.plot_tsne (module) NetExplorer.views.http_api.plannet.autocomplete (module) NetExplorer.views.http_api.plannet.downloader (module) NetExplorer.views.http_api.plannet.error_handler (module) NetExplorer.views.http_api.plannet.get_card (module) NetExplorer.views.http_api.plannet.get_fasta (module) NetExplorer.views.http_api.plannet.map_expression (module) NetExplorer.views.http_api.plannet.show_connections (module) NetExplorer.views.pages.about (module) NetExplorer.views.pages.account (module) NetExplorer.views.pages.blast (module) NetExplorer.views.pages.datasets (module) NetExplorer.views.pages.downloads (module) NetExplorer.views.pages.gene_search (module) NetExplorer.views.pages.index (module) NetExplorer.views.pages.net_explorer (module) NetExplorer.views.pages.path_finder (module) NetExplorer.views.pages.planexp (module) NetExplorer.views.pages.tutorial (module) new_nodes() (NetExplorer.models.neo4j_models.GraphCytoscape method) Node (class in NetExplorer.models.neo4j_models) node (NetExplorer.models.neo4j_models.HasDomain attribute) nodes (NetExplorer.models.neo4j_models.GraphCytoscape attribute) nog_brh (NetExplorer.models.neo4j_models.Homology attribute) nog_eval (NetExplorer.models.neo4j_models.Homology attribute)

O

objects (NetExplorer.models.mysql_models.CellPlotPosition attribute) (NetExplorer.models.mysql_models.ClusterMarkers attribute) (NetExplorer.models.mysql_models.Condition attribute) (NetExplorer.models.mysql_models.ConditionType attribute) (NetExplorer.models.mysql_models.Dataset attribute) (NetExplorer.models.mysql_models.Experiment attribute) (NetExplorer.models.mysql_models.ExperimentDataset attribute) (NetExplorer.models.mysql_models.ExperimentGene attribute) (NetExplorer.models.mysql_models.ExperimentType attribute) (NetExplorer.models.mysql_models.ExpressionCondition attribute) (NetExplorer.models.mysql_models.ExpressionRelative attribute) (NetExplorer.models.mysql_models.RegulatoryLinks attribute) (NetExplorer.models.mysql_models.Sample attribute) (NetExplorer.models.mysql_models.SampleCondition attribute) (NetExplorer.models.mysql_models.UserDatasetPermission attribute) (NetExplorer.models.mysql_models.UserExperimentPermission attribute) (NetExplorer.models.neo4j_models.Document attribute)

oldExperiment (class in NetExplorer.models.neo4j_models) oname (NetExplorer.models.downloaders.ServedFile attribute) orf (NetExplorer.models.neo4j_models.PlanarianContig attribute) orflength (NetExplorer.models.neo4j_models.PlanarianContig attribute)

P

p_end (NetExplorer.models.neo4j_models.HasDomain attribute) p_start (NetExplorer.models.neo4j_models.HasDomain attribute) parameters (NetExplorer.models.neo4j_models.PredInteraction attribute) path_finder() (in module NetExplorer.views.pages.path_finder) path_to_node() (NetExplorer.models.neo4j_models.PlanarianContig method) Pathway (class in NetExplorer.models.neo4j_models) perc (NetExplorer.models.neo4j_models.HasDomain attribute) percentiles (NetExplorer.models.neo4j_models.oldExperiment attribute) pfam_brh (NetExplorer.models.neo4j_models.Homology attribute) pfam_regexp (NetExplorer.models.neo4j_models.Domain attribute), [1] pfam_sc (NetExplorer.models.neo4j_models.Homology attribute) PlanarianContig (class in NetExplorer.models.neo4j_models) PlanarianGene (class in NetExplorer.models.neo4j_models) planexp() (in module NetExplorer.views.pages.planexp) plot() (NetExplorer.models.plots.BarPlot method) (NetExplorer.models.plots.GeneExpPlot method) (NetExplorer.models.plots.HeatmapPlot method) (NetExplorer.models.plots.LinePlot method) (NetExplorer.models.plots.ScatterPlot method) (NetExplorer.models.plots.ViolinPlot method) (NetExplorer.models.plots.VolcanoPlot method)

plot_gene_coexpression() (in module NetExplorer.views.http_api.planexp.plots.plot_gene_coexpression) plot_gene_expression() (in module NetExplorer.views.http_api.planexp.plots.plot_gene_expression) plot_tsne() (in module NetExplorer.views.http_api.planexp.plots.plot_tsne) PlotCreator (class in NetExplorer.models.plots) PlotlyTrace (class in NetExplorer.models.plots) PredInteraction (class in NetExplorer.models.neo4j_models) prednode (NetExplorer.models.neo4j_models.Homology attribute) preferred_database (NetExplorer.models.neo4j_models.PlanarianGene attribute) profile (NetExplorer.models.colors.ColorGenerator attribute) public (NetExplorer.models.mysql_models.Dataset attribute), [1] (NetExplorer.models.mysql_models.Experiment attribute), [1] pvalue (NetExplorer.models.mysql_models.ExpressionRelative attribute), [1]

Q

quick_search() (NetExplorer.models.neo4j_models.GeneSearch method)

R

red (NetExplorer.models.colors.ColorProfiles attribute) red_green (NetExplorer.models.colors.ColorProfiles attribute) reference (NetExplorer.models.neo4j_models.oldExperiment attribute) regulator (NetExplorer.models.mysql_models.RegulatoryLinks attribute), [1] regulatory_links() (in module NetExplorer.views.http_api.planexp.general.regulatory_links)

RegulatoryLinks (class in NetExplorer.models.mysql_models) RegulatoryLinks.DoesNotExist RegulatoryLinks.MultipleObjectsReturned regulatorylinks_set (NetExplorer.models.mysql_models.Dataset attribute) (NetExplorer.models.mysql_models.Experiment attribute) results (NetExplorer.models.gene_ontology.GeneOntologyEnrichment attribute)

S

s_end (NetExplorer.models.neo4j_models.HasDomain attribute) s_start (NetExplorer.models.neo4j_models.HasDomain attribute) Sample (class in NetExplorer.models.mysql_models) sample (NetExplorer.models.mysql_models.CellPlotPosition attribute), [1] (NetExplorer.models.mysql_models.ExpressionAbsolute attribute), [1] (NetExplorer.models.mysql_models.SampleCondition attribute), [1] Sample.DoesNotExist Sample.MultipleObjectsReturned sample_id (NetExplorer.models.mysql_models.CellPlotPosition attribute) (NetExplorer.models.mysql_models.ExpressionAbsolute attribute) (NetExplorer.models.mysql_models.SampleCondition attribute) sample_name (NetExplorer.models.mysql_models.Sample attribute), [1] sample_set (NetExplorer.models.mysql_models.Experiment attribute) SampleCondition (class in NetExplorer.models.mysql_models) SampleCondition.DoesNotExist SampleCondition.MultipleObjectsReturned samplecondition_set (NetExplorer.models.mysql_models.Condition attribute) (NetExplorer.models.mysql_models.Experiment attribute) (NetExplorer.models.mysql_models.Sample attribute) samples (NetExplorer.models.neo4j_models.ExperimentList attribute) ScatterPlot (class in NetExplorer.models.plots) score (NetExplorer.models.mysql_models.RegulatoryLinks attribute), [1] (NetExplorer.models.neo4j_models.Pathway attribute)

search (NetExplorer.models.neo4j_models.WildCard attribute) sequence (NetExplorer.models.neo4j_models.PlanarianContig attribute) (NetExplorer.models.neo4j_models.PlanarianGene attribute) ServedFile (class in NetExplorer.models.downloaders) set_limits() (NetExplorer.models.plots.VolcanoPlot method) show_connections() (in module NetExplorer.views.http_api.plannet.show_connections) smesgene_regexp (NetExplorer.models.neo4j_models.PlanarianGene attribute) sort_results() (in module NetExplorer.views.pages.gene_search) source (NetExplorer.models.mysql_models.RegulatoryLinks attribute), [1] source_symbol (NetExplorer.models.neo4j_models.PredInteraction attribute) start (NetExplorer.models.neo4j_models.PlanarianGene attribute) sterm (NetExplorer.models.neo4j_models.GeneSearch attribute) sterm_database (NetExplorer.models.neo4j_models.GeneSearch attribute) strand (NetExplorer.models.neo4j_models.PlanarianGene attribute) sum_expression (NetExplorer.models.mysql_models.ExpressionCondition attribute), [1] summary (NetExplorer.models.neo4j_models.HumanNode attribute) summary_source (NetExplorer.models.neo4j_models.HumanNode attribute) symbol (NetExplorer.models.neo4j_models.KeggPathway attribute) (NetExplorer.models.neo4j_models.Node attribute) (NetExplorer.models.neo4j_models.PlanarianContig attribute) (NetExplorer.models.neo4j_models.PlanarianGene attribute) symbol_is_empty() (in module NetExplorer.views.helpers.common)

T

target (NetExplorer.models.mysql_models.RegulatoryLinks attribute), [1] (NetExplorer.models.neo4j_models.PredInteraction attribute) title (NetExplorer.models.plots.GeneExpPlot attribute) to_json() (NetExplorer.models.mysql_models.Experiment method) (NetExplorer.models.neo4j_models.GraphCytoscape method) (NetExplorer.models.neo4j_models.oldExperiment method) to_jsondict() (NetExplorer.models.neo4j_models.HasDomain method) (NetExplorer.models.neo4j_models.HumanNode method) (NetExplorer.models.neo4j_models.PlanarianContig method) (NetExplorer.models.neo4j_models.PredInteraction method)

to_response() (NetExplorer.models.downloaders.ServedFile method) trace_names (NetExplorer.models.plots.GeneExpPlot attribute) traces (NetExplorer.models.plots.GeneExpPlot attribute) tutorial() (in module NetExplorer.views.pages.tutorial) type (NetExplorer.models.plots.HeatmapPlot attribute) (NetExplorer.models.plots.LinePlot attribute) (NetExplorer.models.plots.ScatterPlot attribute)

U

units (NetExplorer.models.mysql_models.ExpressionAbsolute attribute), [1] upload_graph() (in module NetExplorer.views.pages.net_explorer) url (NetExplorer.models.mysql_models.Dataset attribute), [1] (NetExplorer.models.mysql_models.Experiment attribute), [1] (NetExplorer.models.neo4j_models.oldExperiment attribute) user (NetExplorer.models.mysql_models.UserDatasetPermission attribute), [1] (NetExplorer.models.mysql_models.UserExperimentPermission attribute), [1] user_id (NetExplorer.models.mysql_models.UserDatasetPermission attribute) (NetExplorer.models.mysql_models.UserExperimentPermission attribute)

UserDatasetPermission (class in NetExplorer.models.mysql_models) UserDatasetPermission.DoesNotExist UserDatasetPermission.MultipleObjectsReturned userdatasetpermission_set (NetExplorer.models.mysql_models.Dataset attribute) UserExperimentPermission (class in NetExplorer.models.mysql_models) UserExperimentPermission.DoesNotExist UserExperimentPermission.MultipleObjectsReturned userexperimentpermission_set (NetExplorer.models.mysql_models.Experiment attribute)

V

ViolinPlot (class in NetExplorer.models.plots)

VolcanoPlot (class in NetExplorer.models.plots)

W

white_green (NetExplorer.models.colors.ColorProfiles attribute) white_red (NetExplorer.models.colors.ColorProfiles attribute)

WildCard (class in NetExplorer.models.neo4j_models) write() (NetExplorer.models.downloaders.ServedFile method) written (NetExplorer.models.downloaders.ServedFile attribute)

X

x (NetExplorer.models.plots.HeatmapPlot attribute)

x_position (NetExplorer.models.mysql_models.CellPlotPosition attribute), [1] xlab (NetExplorer.models.plots.GeneExpPlot attribute)

Y

y (NetExplorer.models.plots.HeatmapPlot attribute) y_position (NetExplorer.models.mysql_models.CellPlotPosition attribute), [1] year (NetExplorer.models.mysql_models.Dataset attribute), [1]

yellow_blue (NetExplorer.models.colors.ColorProfiles attribute) yellow_white (NetExplorer.models.colors.ColorProfiles attribute) ylab (NetExplorer.models.plots.GeneExpPlot attribute)

Z

z (NetExplorer.models.plots.HeatmapPlot attribute)