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B
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C
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D
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E
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F
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G
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H
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M
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O
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P
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R
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S
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T
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U
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V
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W
A
add_GMT_entry() (pygna.output.Output method)
apply_multiple_testing_correction() (in module pygna.output)
B
BlockModel (class in pygna.block_model)
C
calculate_sum() (in module pygna.statistical_comparison)
clean_table() (pygna.elaborators.TableElaboration static method)
close_temporary_table() (pygna.output.Output method)
comparison_empirical_pvalue() (pygna.statistical_comparison.StatisticalComparison method)
comparison_random_walk() (in module pygna.statistical_comparison)
comparison_shortest_path() (in module pygna.statistical_comparison)
convert_e2s() (pygna.converters.Converters class method)
convert_s2e() (pygna.converters.Converters class method)
Converters (class in pygna.converters)
create_comparison_table_empirical() (pygna.output.Output method)
create_GMT_output() (pygna.output.Output method)
create_graph() (pygna.block_model.BlockModel method)
(pygna.degree_model.DegreeModel method)
create_st_table_empirical() (pygna.output.Output method)
CsvToCsvEnriched (class in pygna.converters)
CsvToGmt (class in pygna.converters)
D
DegreeModel (class in pygna.degree_model)
DiffusionTest (class in pygna.statistical_diffusion)
E
empirical_pvalue() (pygna.statistical_diffusion.DiffusionTest method)
(pygna.statistical_test.StatisticalTest method)
F
filter_table() (pygna.elaborators.TableElaboration static method)
G
generate_graph_from_sm() (in module pygna.block_model)
generate_graph_vip() (in module pygna.degree_model)
generate_sbm_network() (in module pygna.block_model)
geneset_internal_degree_statistic() (in module pygna.statistical_test)
geneset_localisation_statistic() (in module pygna.statistical_test)
geneset_localisation_statistic_median() (in module pygna.statistical_test)
geneset_module_statistic() (in module pygna.statistical_test)
geneset_RW_statistic() (in module pygna.statistical_test)
geneset_total_degree_statistic() (in module pygna.statistical_test)
get_comparison_null_distribution() (pygna.statistical_comparison.StatisticalComparison method)
get_comparison_null_distribution_mp() (pygna.statistical_comparison.StatisticalComparison method)
get_data() (pygna.converters.CsvToCsvEnriched method)
(pygna.reading_class.ReadCsv method)
(pygna.reading_class.ReadDistanceMatrix method)
(pygna.reading_class.ReadGmt method)
(pygna.reading_class.ReadTsv method)
(pygna.reading_class.ReadTxt method)
(pygna.reading_class.ReadingData method)
get_geneset() (pygna.reading_class.ReadGmt method)
get_network() (pygna.reading_class.ReadTsv method)
get_null_distribution() (pygna.statistical_diffusion.DiffusionTest method)
(pygna.statistical_test.StatisticalTest method)
get_null_distribution_mp() (pygna.statistical_diffusion.DiffusionTest method)
(pygna.statistical_test.StatisticalTest method)
GmtToGmtEnriched (class in pygna.converters)
GroupGmt (class in pygna.converters)
H
hotnet_diffusion_statistic() (in module pygna.statistical_diffusion)
M
map_table2matrix() (in module pygna.statistical_diffusion)
O
Output (class in pygna.output)
P
plot_adjacency() (in module pygna.degree_model)
plot_bm_graph() (in module pygna.block_model)
plot_connected_components() (in module pygna.diagnostic)
plot_degree() (in module pygna.diagnostic)
plot_diffusion_matrix() (in module pygna.diagnostic)
plot_graph() (pygna.block_model.BlockModel method)
plot_null_distribution() (in module pygna.diagnostic)
plot_vip_graph() (in module pygna.degree_model)
print_GMT() (in module pygna.output)
PygnaFigure (class in pygna.plots)
R
ReadCsv (class in pygna.reading_class)
ReadDistanceMatrix (class in pygna.reading_class)
ReadGmt (class in pygna.reading_class)
ReadingData (class in pygna.reading_class)
ReadTsv (class in pygna.reading_class)
ReadTxt (class in pygna.reading_class)
S
set_bm() (pygna.block_model.BlockModel method)
set_diffusion_matrix() (pygna.output.Output method)
set_nodes() (pygna.block_model.BlockModel method)
(pygna.degree_model.DegreeModel method)
set_nodes_in_block() (pygna.block_model.BlockModel method)
set_nodes_in_block_percentage() (pygna.block_model.BlockModel method)
StatisticalComparison (class in pygna.statistical_comparison)
StatisticalTest (class in pygna.statistical_test)
T
TableElaboration (class in pygna.elaborators)
U
update_comparison_table_empirical() (pygna.output.Output method)
update_st_table_empirical() (pygna.output.Output method)
V
VolcanoPlot (class in pygna.plots)
W
weights_diffusion_statistic() (in module pygna.statistical_diffusion)
write_cluster_genelist() (pygna.block_model.BlockModel method)
write_genelist() (pygna.degree_model.DegreeModel method)
write_graph_summary() (in module pygna.output)
write_network() (pygna.block_model.BlockModel method)
(pygna.degree_model.DegreeModel method)
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