Index

A

AbstractPlottingOperation (class in GSForge.plots.abstract_plot_models) active_count_variable (GSForge.models.Interface property) adjoint_distributions (GSForge.plots.gem.GenewiseAggregateScatter attribute) alpha (GSForge.operations.prospectors.BorutaProspector attribute) AnnotatedGEM (class in GSForge.models)

annotation_mask (GSForge.models.Interface attribute) annotation_variables (GSForge.models.Interface attribute) apply_default_opts (GSForge.plots.abstract_plot_models.AbstractPlottingOperation attribute) as_dict() (GSForge.models.GeneSetCollection method) axis_functions (GSForge.plots.gem.GenewiseAggregateScatter attribute)

B

beta_matrix() (GSForge.utils.generate_gem.RandomGEMSimulator method) bokeh_opts (GSForge.plots.gem.GeneCountOverTime property) bokeh_opts() (GSForge.plots.abstract_plot_models.AbstractPlottingOperation static method) (GSForge.plots.collections.WithinCollectionOverlapHeatMap static method) (GSForge.plots.gem.EmpiricalCumulativeDistribution static method) (GSForge.plots.gem.GeneVsCountsScatter static method) (GSForge.plots.gem.GenewiseAggregateScatter static method) (GSForge.plots.gem.GroupedGeneCovariance static method) (GSForge.plots.gem.SamplewiseDistributions static method) (GSForge.plots.results.MeanVsLFC static method) (GSForge.plots.results.Volcano static method)

BorutaProspector (class in GSForge.operations.prospectors) build_count_matrix() (GSForge.utils.generate_gem.RandomGEMSimulator method) build_membership_series() (GSForge.plots.collections.UpsetPlotInterface static method)

C

CallableInterface (class in GSForge.models) canvas_opts (GSForge.plots.gem.RasterGEM attribute) ChiSquaredTest (class in GSForge.operations.prospectors) cmap (GSForge.plots.gem.EmpiricalCumulativeDistribution attribute) (GSForge.plots.gem.RasterGEM attribute) (GSForge.plots.gem.SamplewiseDistributions attribute) colorized_gem_raster() (GSForge.plots.gem.RasterGEM static method) construct_standard_specification() (GSForge.models.GeneSetCollection method)

count_array_name (GSForge.models.AnnotatedGEM attribute) count_array_names (GSForge.models.AnnotatedGEM property) count_mask (GSForge.models.Interface attribute) count_set_terms() (in module GSForge.utils.enrichment) count_transform (GSForge.models.Interface attribute) count_variable (GSForge.models.Interface attribute) create_plot_dataframe() (GSForge.plots.gem.GeneCountOverTime static method) create_spread_dataframe() (GSForge.plots.gem.GeneCountOverTime static method)

D

data (GSForge.models.AnnotatedGEM attribute) (GSForge.models.GeneSet attribute) datashade (GSForge.plots.gem.EmpiricalCumulativeDistribution attribute) (GSForge.plots.gem.GenewiseAggregateScatter attribute) (GSForge.plots.gem.GroupedGeneCovariance attribute) (GSForge.plots.gem.SamplewiseDistributions attribute)

DGE_DEFAULT_KWARGS (GSForge.plots.abstract_plot_models.ResultPlottingOperation attribute) difference() (GSForge.models.GeneSetCollection method) dispersion_variable (GSForge.plots.gem.GeneCountOverTime attribute) dynspread (GSForge.plots.gem.EmpiricalCumulativeDistribution attribute) (GSForge.plots.gem.GenewiseAggregateScatter attribute) (GSForge.plots.gem.GroupedGeneCovariance attribute) (GSForge.plots.gem.SamplewiseDistributions attribute)

E

EmpiricalCumulativeDistribution (class in GSForge.plots.gem) enrichment_score() (in module GSForge.utils.enrichment)

estimator (GSForge.operations.prospectors.BorutaProspector attribute) evaluate_kde() (GSForge.plots.gem.SamplewiseDistributions static method)

F

FClassificationTest (class in GSForge.operations.prospectors) from_bool_array() (GSForge.models.GeneSet class method) from_files() (GSForge.models.AnnotatedGEM class method) from_folder() (GSForge.models.GeneSetCollection class method) from_gene_array() (GSForge.models.GeneSet class method) from_GeneSets() (GSForge.models.GeneSet class method)

from_geo_id() (GSForge.models.AnnotatedGEM class method) from_netcdf() (GSForge.models.AnnotatedGEM class method) (GSForge.models.GeneSet class method) from_pandas() (GSForge.models.AnnotatedGEM class method) (GSForge.models.GeneSet class method) from_specification() (GSForge.models.GeneSetCollection class method) from_xarray_dataset() (GSForge.models.GeneSet class method)

G

gem (GSForge.models.GeneSetCollection attribute) (GSForge.models.Interface attribute) gem_raster() (GSForge.plots.gem.RasterGEM static method) gene_index (GSForge.models.AnnotatedGEM property) (GSForge.models.GeneSet property) gene_index_name (GSForge.models.AnnotatedGEM attribute) (GSForge.models.GeneSet attribute) (GSForge.models.Interface property) gene_set_collection (GSForge.models.Interface attribute) gene_set_collection_to_support_dataframe() (in module GSForge.utils.converters) gene_set_mode (GSForge.models.Interface attribute) gene_sets_to_csv_files() (GSForge.models.GeneSetCollection method) gene_sets_to_dataframes() (GSForge.models.GeneSetCollection method) gene_sets_to_excel_sheet() (GSForge.models.GeneSetCollection method) GeneCountOverTime (class in GSForge.plots.gem) GeneSet (class in GSForge.models) GeneSetCollection (class in GSForge.models) GeneVsCountsScatter (class in GSForge.plots.gem) genewise_scatter() (GSForge.plots.gem.GeneVsCountsScatter static method) GenewiseAggregateScatter (class in GSForge.plots.gem) get_default_options() (GSForge.plots.abstract_plot_models.AbstractPlottingOperation method) get_gem_data (class in GSForge.operations.core) get_gem_data() (GSForge.models.Interface method) get_gene_index() (GSForge.models.Interface method) get_genes_by_term() (in module GSForge.utils.enrichment) get_genes_by_threshold() (GSForge.models.GeneSet method) get_param_process_overlap_kwargs() (GSForge.plots.abstract_plot_models.AbstractPlottingOperation method) get_plot_dataframe() (GSForge.plots.gem.GeneCountOverTime method) get_sample_index() (GSForge.models.Interface method) get_selection_indices (GSForge.models.Interface property) get_spread_dataframe() (GSForge.plots.gem.GeneCountOverTime method) get_support() (GSForge.models.GeneSet method) (GSForge.models.GeneSetCollection method) get_top_n_genes() (GSForge.models.GeneSet method) group_variable (GSForge.plots.gem.GroupedGeneCovariance attribute) grouped_data (GSForge.plots.gem.GroupedGeneCovariance attribute) grouped_mean_scatter() (GSForge.plots.gem.GroupedGeneCovariance static method)

GroupedGeneCovariance (class in GSForge.plots.gem) GSForge module GSForge.models module GSForge.operations module GSForge.operations.analytics module GSForge.operations.core module GSForge.operations.normalizations module GSForge.operations.prospectors module GSForge.plots module GSForge.plots.abstract_plot_models module GSForge.plots.annotations module GSForge.plots.collections module GSForge.plots.gem module GSForge.plots.results module GSForge.utils module GSForge.utils.converters module GSForge.utils.enrichment module GSForge.utils.generate_gem module GSForge.utils.R_interface module

H

hue (GSForge.plots.gem.GeneVsCountsScatter attribute) (GSForge.plots.gem.RasterGEM attribute) hue_colors (GSForge.plots.gem.EmpiricalCumulativeDistribution attribute) (GSForge.plots.gem.SamplewiseDistributions attribute)

hue_key (GSForge.plots.gem.EmpiricalCumulativeDistribution attribute) (GSForge.plots.gem.SamplewiseDistributions attribute)

I

infer_kwarg_defaults_from_data() (GSForge.plots.abstract_plot_models.ResultPlottingOperation class method) infer_variables() (GSForge.models.AnnotatedGEM method)

Interface (class in GSForge.models) InterfacePlottingBase (class in GSForge.plots.abstract_plot_models) intersection() (GSForge.models.GeneSetCollection method)

J

joint_difference() (GSForge.models.GeneSetCollection method)

K

kde_kwargs (GSForge.plots.gem.SamplewiseDistributions attribute) kde_linespace() (GSForge.plots.gem.SamplewiseDistributions static method)

kde_sample_size (GSForge.plots.gem.SamplewiseDistributions attribute) ks_enrichment_score() (in module GSForge.utils.enrichment)

L

label_selected_genes (GSForge.plots.results.MeanVsLFC attribute) (GSForge.plots.results.Volcano attribute) length_variable (GSForge.operations.normalizations.ReadsPerKilobaseMillion attribute) log2_output (GSForge.plots.gem.GeneCountOverTime attribute)

log_fold_change (GSForge.plots.gem.GeneCountOverTime attribute) log_fold_change_cutoff (GSForge.plots.results.MeanVsLFC attribute) (GSForge.plots.results.Volcano attribute) log_fold_change_var (GSForge.plots.results.MeanVsLFC attribute) (GSForge.plots.results.Volcano attribute)

M

matplotlib_opts() (GSForge.plots.abstract_plot_models.AbstractPlottingOperation static method) (GSForge.plots.collections.WithinCollectionOverlapHeatMap static method) (GSForge.plots.gem.EmpiricalCumulativeDistribution static method) (GSForge.plots.gem.GeneVsCountsScatter static method) (GSForge.plots.gem.GenewiseAggregateScatter static method) (GSForge.plots.gem.GroupedGeneCovariance static method) (GSForge.plots.gem.SamplewiseDistributions static method) (GSForge.plots.results.MeanVsLFC static method) (GSForge.plots.results.Volcano static method) max_iter (GSForge.operations.prospectors.BorutaProspector attribute) mean_value_var (GSForge.plots.results.MeanVsLFC attribute) mean_vs_lfc() (GSForge.plots.results.MeanVsLFC static method) MeanVsLFC (class in GSForge.plots.results) merge_specifications() (GSForge.models.GeneSetCollection static method) min_overlap_size (GSForge.plots.collections.UpsetPlotInterface attribute) mode (GSForge.plots.collections.WithinCollectionOverlapHeatMap attribute) model (GSForge.operations.analytics.mProbes attribute) (GSForge.operations.analytics.nFDR attribute) (GSForge.operations.analytics.RankGenesByModel attribute) module GSForge GSForge.models GSForge.operations GSForge.operations.analytics GSForge.operations.core GSForge.operations.normalizations GSForge.operations.prospectors GSForge.plots GSForge.plots.abstract_plot_models GSForge.plots.annotations GSForge.plots.collections GSForge.plots.gem GSForge.plots.results GSForge.utils GSForge.utils.converters GSForge.utils.enrichment GSForge.utils.generate_gem GSForge.utils.R_interface

mProbes (class in GSForge.operations.analytics) mProbes() (GSForge.operations.analytics.mProbes static method)

N

n_estimators (GSForge.operations.prospectors.BorutaProspector attribute) n_genes (GSForge.utils.generate_gem.RandomGEMSimulator attribute) n_iterations (GSForge.operations.analytics.mProbes attribute) (GSForge.operations.analytics.nFDR attribute) (GSForge.operations.analytics.RankGenesByModel attribute) n_negative_control_genes (GSForge.utils.generate_gem.RandomGEMSimulator attribute) n_random_noise_dims (GSForge.utils.generate_gem.RandomGEMSimulator attribute) n_samples (GSForge.utils.generate_gem.RandomGEMSimulator attribute) n_signal_dims (GSForge.utils.generate_gem.RandomGEMSimulator attribute) n_signal_noise_dims (GSForge.utils.generate_gem.RandomGEMSimulator attribute) n_strongly_expressed_genes (GSForge.utils.generate_gem.RandomGEMSimulator attribute) name (GSForge.models.AnnotatedGEM attribute) (GSForge.models.CallableInterface attribute) (GSForge.models.GeneSet attribute) (GSForge.models.GeneSetCollection attribute) (GSForge.models.Interface attribute) (GSForge.operations.analytics.mProbes attribute) (GSForge.operations.analytics.nFDR attribute) (GSForge.operations.analytics.RankGenesByModel attribute) (GSForge.operations.core.get_gem_data attribute) (GSForge.operations.normalizations.ReadsPerKilobaseMillion attribute) (GSForge.operations.normalizations.UpperQuartile attribute) (GSForge.operations.prospectors.BorutaProspector attribute) (GSForge.operations.prospectors.ChiSquaredTest attribute) (GSForge.operations.prospectors.FClassificationTest attribute) (GSForge.plots.abstract_plot_models.AbstractPlottingOperation attribute) (GSForge.plots.abstract_plot_models.InterfacePlottingBase attribute) (GSForge.plots.abstract_plot_models.ResultPlottingOperation attribute) (GSForge.plots.collections.UpsetPlotInterface attribute) (GSForge.plots.collections.WithinCollectionOverlapHeatMap attribute) (GSForge.plots.gem.EmpiricalCumulativeDistribution attribute) (GSForge.plots.gem.GeneCountOverTime attribute) (GSForge.plots.gem.GeneVsCountsScatter attribute) (GSForge.plots.gem.GenewiseAggregateScatter attribute) (GSForge.plots.gem.GroupedGeneCovariance attribute) (GSForge.plots.gem.RasterGEM attribute) (GSForge.plots.gem.SamplewiseDistributions attribute) (GSForge.plots.results.MeanVsLFC attribute) (GSForge.plots.results.Volcano attribute) (GSForge.utils.generate_gem.RandomGEMSimulator attribute)

nFDR (class in GSForge.operations.analytics) nFDR() (GSForge.operations.analytics.nFDR static method) noise_and_design_correlation_matrix() (GSForge.utils.generate_gem.RandomGEMSimulator method) noise_matrix() (GSForge.utils.generate_gem.RandomGEMSimulator method) np_reads_per_kilobase_million() (GSForge.operations.normalizations.ReadsPerKilobaseMillion static method) np_upper_quartile() (GSForge.operations.normalizations.UpperQuartile static method)

O

output_type (GSForge.operations.core.get_gem_data attribute)

P

p_value_cutoff (GSForge.plots.results.MeanVsLFC attribute) (GSForge.plots.results.Volcano attribute) p_value_var (GSForge.plots.results.MeanVsLFC attribute) (GSForge.plots.results.Volcano attribute) pairwise_intersection() (GSForge.models.GeneSetCollection method) pairwise_percent_intersection() (GSForge.models.GeneSetCollection method) pairwise_unions() (GSForge.models.GeneSetCollection method) parse_boruta_model() (in module GSForge.operations.prospectors) perc (GSForge.operations.prospectors.BorutaProspector attribute)

plot_as_scatter() (GSForge.plots.gem.GeneCountOverTime method) plot_dispersion_spread() (GSForge.plots.gem.GeneCountOverTime method) plot_mean_curve() (GSForge.plots.gem.GeneCountOverTime method) plot_options (GSForge.plots.abstract_plot_models.AbstractPlottingOperation attribute) (GSForge.plots.gem.RasterGEM attribute) plot_sample_wise_ecdf() (GSForge.plots.gem.EmpiricalCumulativeDistribution static method) plot_sample_wise_kde() (GSForge.plots.gem.SamplewiseDistributions class method) process_set_operation_specification() (GSForge.models.GeneSetCollection method) Py_counts_to_R() (in module GSForge.utils.R_interface) Py_labels_to_R() (in module GSForge.utils.R_interface)

R

R_counts_to_Py() (in module GSForge.utils.R_interface) random_noise_sigma (GSForge.utils.generate_gem.RandomGEMSimulator attribute) random_state (GSForge.operations.prospectors.BorutaProspector attribute) RandomGEMSimulator (class in GSForge.utils.generate_gem)

rank_genes_by_model() (GSForge.operations.analytics.RankGenesByModel static method) RankGenesByModel (class in GSForge.operations.analytics) RasterGEM (class in GSForge.plots.gem) ReadsPerKilobaseMillion (class in GSForge.operations.normalizations) ResultPlottingOperation (class in GSForge.plots.abstract_plot_models)

S

sample_colormap (GSForge.plots.gem.EmpiricalCumulativeDistribution attribute) (GSForge.plots.gem.SamplewiseDistributions attribute) sample_index (GSForge.models.AnnotatedGEM property) sample_index_name (GSForge.models.AnnotatedGEM attribute) (GSForge.models.Interface property) sample_subset (GSForge.models.Interface attribute) SamplewiseDistributions (class in GSForge.plots.gem) save() (GSForge.models.AnnotatedGEM method) (GSForge.models.GeneSetCollection method) save_as_netcdf() (GSForge.models.GeneSet method) scatter_dist() (GSForge.plots.gem.GenewiseAggregateScatter static method)

scatter_dist_by_mappings() (GSForge.plots.gem.GenewiseAggregateScatter static method) selected_gene (GSForge.plots.gem.GeneCountOverTime attribute) selected_gene_sets (GSForge.models.Interface attribute) selected_genes (GSForge.models.Interface attribute) set_support_by_genes() (GSForge.models.GeneSet method) set_support_from_boolean_array() (GSForge.models.GeneSet method) single_object (GSForge.operations.core.get_gem_data attribute) soft_max (GSForge.plots.gem.GeneVsCountsScatter attribute) source (GSForge.plots.abstract_plot_models.ResultPlottingOperation attribute) summarize_gene_sets() (GSForge.models.GeneSetCollection method) support_exists (GSForge.models.GeneSet property) support_index_name (GSForge.models.GeneSet attribute)

T

time_variable (GSForge.plots.gem.GeneCountOverTime attribute) to_dataframe() (GSForge.models.GeneSet method) transient_log_handler() (in module GSForge.utils)

treatment_colormap (GSForge.plots.gem.GeneCountOverTime attribute) treatment_variable (GSForge.plots.gem.GeneCountOverTime attribute) two_step (GSForge.operations.prospectors.BorutaProspector attribute)

U

union() (GSForge.models.GeneSetCollection method) UpperQuartile (class in GSForge.operations.normalizations)

upset_kwargs (GSForge.plots.collections.UpsetPlotInterface attribute) UpsetPlotInterface (class in GSForge.plots.collections)

V

verbose (GSForge.operations.prospectors.BorutaProspector attribute)

Volcano (class in GSForge.plots.results) volcano() (GSForge.plots.results.Volcano static method)

W

within_collection_overlap() (GSForge.plots.collections.WithinCollectionOverlapHeatMap static method)

WithinCollectionOverlapHeatMap (class in GSForge.plots.collections)

X

x_axis_selector (GSForge.plots.gem.GenewiseAggregateScatter attribute) x_axis_transform (GSForge.plots.gem.EmpiricalCumulativeDistribution attribute) x_count_data (GSForge.models.Interface property)

x_group_label (GSForge.plots.gem.GroupedGeneCovariance attribute) xr_reads_per_kilobase_million() (GSForge.operations.normalizations.ReadsPerKilobaseMillion static method) xr_upper_quartile() (GSForge.operations.normalizations.UpperQuartile static method) xrarray_gem_from_pandas() (GSForge.models.AnnotatedGEM static method)

Y

y_annotation_data (GSForge.models.Interface property)

y_axis_selector (GSForge.plots.gem.GenewiseAggregateScatter attribute) y_group_label (GSForge.plots.gem.GroupedGeneCovariance attribute)