Index

_

__init__() (moonstone.analysis.differential_analysis.DifferentialAnalysis method) (moonstone.filtering.basics_filtering.NamesFiltering method) (moonstone.filtering.basics_filtering.NaNPercentageFiltering method) (moonstone.filtering.basics_filtering.NoCountsFiltering method) (moonstone.filtering.basics_filtering.NumberOfDifferentValuesFiltering method) (moonstone.filtering.mean_filtering.MeanFiltering method) (moonstone.filtering.taxonomy_filtering.TaxonomyMeanFiltering method) (moonstone.filtering.taxonomy_filtering.TaxonomyNamesFiltering method) (moonstone.normalization.counts.geometric_mean.GeometricMeanNormalization method) (moonstone.normalization.counts.random_selection.RandomSelection method) (moonstone.normalization.counts.random_selection.TaxonomyRandomSelection method) (moonstone.normalization.counts.total_counts.TotalCountsNormalization method) (moonstone.normalization.processed.scaling_normalization.StandardScaler method) (moonstone.parsers.counts.genes.GeneCountsParser method) (moonstone.parsers.counts.picrust2.Picrust2PathwaysParser method) (moonstone.parsers.counts.taxonomy.kraken2.SunbeamKraken2Parser method) (moonstone.parsers.counts.taxonomy.metaphlan.BaseMetaphlanParser method) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan2Parser method) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan3Parser method) (moonstone.parsers.counts.taxonomy.qiime.Qiime2Parser method) (moonstone.parsers.metadata.MetadataParser method) (moonstone.parsers.metadata.YAMLBasedMetadataParser method) (moonstone.plot.counts.PlotCountsStats method) (moonstone.plot.counts.PlotTaxonomyCounts method) (moonstone.plot.metadata.PlotMetadataStats method)

A

available_tests (moonstone.analysis.differential_analysis.DifferentialAnalysis attribute)

B

BaseMetaphlanParser (class in moonstone.parsers.counts.taxonomy.metaphlan)

C

calculating_and_substracting_mean_row() (moonstone.normalization.counts.geometric_mean.GeometricMeanNormalization method) compare_difference_between_two_levels() (moonstone.parsers.counts.taxonomy.metaphlan.BaseMetaphlanParser method) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan2Parser method) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan3Parser method)

compute_prevalence_series() (moonstone.plot.counts.PlotTaxonomyCounts method) compute_relative_abundance_dataframe() (moonstone.plot.counts.PlotTaxonomyCounts method) compute_threshold_best_n_percent() (moonstone.filtering.mean_filtering.MeanFiltering method) corrected_p_values() (moonstone.analysis.differential_analysis.DifferentialAnalysis method)

D

dataframe() (moonstone.parsers.counts.genes.GeneCountsParser property) (moonstone.parsers.counts.picrust2.Picrust2PathwaysParser property) (moonstone.parsers.counts.taxonomy.kraken2.SunbeamKraken2Parser property) (moonstone.parsers.counts.taxonomy.metaphlan.BaseMetaphlanParser property) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan2Parser property) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan3Parser property) (moonstone.parsers.counts.taxonomy.qiime.Qiime2Parser property) (moonstone.parsers.metadata.MetadataParser property)

DEFAULT_COLORSCALE (moonstone.parsers.metadata.MetadataParser attribute) differential_analysis_by_feature() (moonstone.analysis.differential_analysis.DifferentialAnalysis method) DifferentialAnalysis (class in moonstone.analysis.differential_analysis)

F

filter() (moonstone.filtering.basics_filtering.NamesFiltering method) (moonstone.filtering.basics_filtering.NaNPercentageFiltering method) (moonstone.filtering.basics_filtering.NoCountsFiltering method) (moonstone.filtering.basics_filtering.NumberOfDifferentValuesFiltering method) (moonstone.filtering.mean_filtering.MeanFiltering method) (moonstone.filtering.taxonomy_filtering.TaxonomyMeanFiltering method) (moonstone.filtering.taxonomy_filtering.TaxonomyNamesFiltering method)

filtered_df() (moonstone.filtering.basics_filtering.NamesFiltering property) (moonstone.filtering.basics_filtering.NaNPercentageFiltering property) (moonstone.filtering.basics_filtering.NoCountsFiltering property) (moonstone.filtering.basics_filtering.NumberOfDifferentValuesFiltering property) (moonstone.filtering.mean_filtering.MeanFiltering property) (moonstone.filtering.taxonomy_filtering.TaxonomyMeanFiltering property) (moonstone.filtering.taxonomy_filtering.TaxonomyNamesFiltering property)

G

GeneCountsParser (class in moonstone.parsers.counts.genes) generate_report_data() (moonstone.filtering.basics_filtering.NamesFiltering method) (moonstone.filtering.basics_filtering.NaNPercentageFiltering method) (moonstone.filtering.basics_filtering.NoCountsFiltering method) (moonstone.filtering.basics_filtering.NumberOfDifferentValuesFiltering method) (moonstone.filtering.mean_filtering.MeanFiltering method) (moonstone.filtering.taxonomy_filtering.TaxonomyMeanFiltering method) (moonstone.filtering.taxonomy_filtering.TaxonomyNamesFiltering method) (moonstone.normalization.counts.geometric_mean.GeometricMeanNormalization method) (moonstone.normalization.counts.random_selection.RandomSelection method) (moonstone.normalization.counts.random_selection.TaxonomyRandomSelection method) (moonstone.normalization.counts.total_counts.TotalCountsNormalization method)

GeometricMeanNormalization (class in moonstone.normalization.counts.geometric_mean) get_stats() (moonstone.parsers.metadata.MetadataParser method)

H

header (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan2Parser attribute) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan3Parser attribute)

L

log_df() (moonstone.normalization.counts.geometric_mean.GeometricMeanNormalization method)

M

MeanFiltering (class in moonstone.filtering.mean_filtering) MetadataParser (class in moonstone.parsers.metadata) Metaphlan2Parser (class in moonstone.parsers.counts.taxonomy.metaphlan) Metaphlan3Parser (class in moonstone.parsers.counts.taxonomy.metaphlan) module moonstone.analysis.differential_analysis moonstone.filtering.basics_filtering moonstone.filtering.mean_filtering moonstone.filtering.taxonomy_filtering moonstone.normalization.counts.geometric_mean moonstone.normalization.counts.random_selection moonstone.normalization.counts.total_counts moonstone.normalization.processed.scaling_normalization moonstone.parsers.counts.genes moonstone.parsers.counts.picrust2 moonstone.parsers.counts.taxonomy.kraken2 moonstone.parsers.counts.taxonomy.metaphlan moonstone.parsers.counts.taxonomy.qiime moonstone.parsers.metadata moonstone.analysis.differential_analysis module moonstone.filtering.basics_filtering module

moonstone.filtering.mean_filtering module moonstone.filtering.taxonomy_filtering module moonstone.normalization.counts.geometric_mean module moonstone.normalization.counts.random_selection module moonstone.normalization.counts.total_counts module moonstone.normalization.processed.scaling_normalization module moonstone.parsers.counts.genes module moonstone.parsers.counts.picrust2 module moonstone.parsers.counts.taxonomy.kraken2 module moonstone.parsers.counts.taxonomy.metaphlan module moonstone.parsers.counts.taxonomy.qiime module moonstone.parsers.metadata module

N

NamesFiltering (class in moonstone.filtering.basics_filtering) NaNPercentageFiltering (class in moonstone.filtering.basics_filtering) NCBI_tax_column (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan3Parser attribute) new_otu_id_name (moonstone.parsers.counts.taxonomy.kraken2.SunbeamKraken2Parser attribute) NoCountsFiltering (class in moonstone.filtering.basics_filtering) non_zero_df() (moonstone.normalization.counts.geometric_mean.GeometricMeanNormalization method) normalize() (moonstone.normalization.counts.geometric_mean.GeometricMeanNormalization method) (moonstone.normalization.counts.random_selection.RandomSelection method) (moonstone.normalization.counts.random_selection.TaxonomyRandomSelection method) (moonstone.normalization.counts.total_counts.TotalCountsNormalization method)

normalized_df() (moonstone.normalization.counts.geometric_mean.GeometricMeanNormalization property) (moonstone.normalization.counts.random_selection.RandomSelection property) (moonstone.normalization.counts.random_selection.TaxonomyRandomSelection property) (moonstone.normalization.counts.total_counts.TotalCountsNormalization property) number_columns_to_skip() (moonstone.analysis.differential_analysis.DifferentialAnalysis property) NumberOfDifferentValuesFiltering (class in moonstone.filtering.basics_filtering)

P

Picrust2PathwaysParser (class in moonstone.parsers.counts.picrust2) plot_age() (moonstone.plot.metadata.PlotMetadataStats method) plot_category_distribution() (moonstone.plot.metadata.PlotMetadataStats method) PLOT_CLASS (moonstone.parsers.counts.taxonomy.kraken2.SunbeamKraken2Parser attribute) (moonstone.parsers.counts.taxonomy.metaphlan.BaseMetaphlanParser attribute) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan2Parser attribute) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan3Parser attribute) (moonstone.parsers.counts.taxonomy.qiime.Qiime2Parser attribute) plot_mean_distribution() (moonstone.plot.counts.PlotCountsStats method) plot_most_abundant_taxa() (moonstone.plot.counts.PlotTaxonomyCounts method) plot_most_prevalent_taxa() (moonstone.plot.counts.PlotTaxonomyCounts method) plot_sample_composition_most_abundant_taxa() (moonstone.plot.counts.PlotTaxonomyCounts method)

plot_sex() (moonstone.plot.metadata.PlotMetadataStats method) PlotCountsStats (class in moonstone.plot.counts) PlotMetadataStats (class in moonstone.plot.metadata) PlotTaxonomyCounts (class in moonstone.plot.counts) plotter() (moonstone.parsers.counts.genes.GeneCountsParser property) (moonstone.parsers.counts.picrust2.Picrust2PathwaysParser property) (moonstone.parsers.counts.taxonomy.kraken2.SunbeamKraken2Parser property) (moonstone.parsers.counts.taxonomy.metaphlan.BaseMetaphlanParser property) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan2Parser property) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan3Parser property) (moonstone.parsers.counts.taxonomy.qiime.Qiime2Parser property) (moonstone.parsers.metadata.MetadataParser property) prevalence_series() (moonstone.plot.counts.PlotTaxonomyCounts property)

Q

Qiime2Parser (class in moonstone.parsers.counts.taxonomy.qiime)

R

RandomSelection (class in moonstone.normalization.counts.random_selection) rank_level() (moonstone.parsers.counts.taxonomy.kraken2.SunbeamKraken2Parser property) (moonstone.parsers.counts.taxonomy.metaphlan.BaseMetaphlanParser property) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan2Parser property) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan3Parser property) (moonstone.parsers.counts.taxonomy.qiime.Qiime2Parser property) relative_abundance_dataframe() (moonstone.plot.counts.PlotTaxonomyCounts property) remove_duplicates() (moonstone.parsers.counts.taxonomy.metaphlan.BaseMetaphlanParser method) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan2Parser method) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan3Parser method) remove_zero_and_apply_log() (moonstone.normalization.counts.geometric_mean.GeometricMeanNormalization method) removed_zero_df() (moonstone.normalization.counts.geometric_mean.GeometricMeanNormalization property) report_data() (moonstone.filtering.basics_filtering.NamesFiltering property) (moonstone.filtering.basics_filtering.NaNPercentageFiltering property) (moonstone.filtering.basics_filtering.NoCountsFiltering property) (moonstone.filtering.basics_filtering.NumberOfDifferentValuesFiltering property) (moonstone.filtering.mean_filtering.MeanFiltering property) (moonstone.filtering.taxonomy_filtering.TaxonomyMeanFiltering property) (moonstone.filtering.taxonomy_filtering.TaxonomyNamesFiltering property) (moonstone.normalization.counts.geometric_mean.GeometricMeanNormalization property) (moonstone.normalization.counts.random_selection.RandomSelection property) (moonstone.normalization.counts.random_selection.TaxonomyRandomSelection property) (moonstone.normalization.counts.total_counts.TotalCountsNormalization property)

rows_differences() (moonstone.parsers.counts.taxonomy.metaphlan.BaseMetaphlanParser method) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan2Parser method) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan3Parser method)

S

scale() (moonstone.normalization.processed.scaling_normalization.StandardScaler method) scaled_x() (moonstone.normalization.processed.scaling_normalization.StandardScaler property) scaling_factors() (moonstone.normalization.counts.geometric_mean.GeometricMeanNormalization property) (moonstone.normalization.counts.total_counts.TotalCountsNormalization property) split_taxa_fill_none() (moonstone.parsers.counts.taxonomy.kraken2.SunbeamKraken2Parser method) (moonstone.parsers.counts.taxonomy.metaphlan.BaseMetaphlanParser method) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan2Parser method) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan3Parser method) (moonstone.parsers.counts.taxonomy.qiime.Qiime2Parser method)

StandardScaler (class in moonstone.normalization.processed.scaling_normalization) SunbeamKraken2Parser (class in moonstone.parsers.counts.taxonomy.kraken2)

T

taxa_column (moonstone.parsers.counts.taxonomy.kraken2.SunbeamKraken2Parser attribute) (moonstone.parsers.counts.taxonomy.metaphlan.BaseMetaphlanParser attribute) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan2Parser attribute) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan3Parser attribute) (moonstone.parsers.counts.taxonomy.qiime.Qiime2Parser attribute) taxonomical_names (moonstone.parsers.counts.taxonomy.kraken2.SunbeamKraken2Parser attribute) (moonstone.parsers.counts.taxonomy.metaphlan.BaseMetaphlanParser attribute) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan2Parser attribute) (moonstone.parsers.counts.taxonomy.metaphlan.Metaphlan3Parser attribute) (moonstone.parsers.counts.taxonomy.qiime.Qiime2Parser attribute)

TaxonomyMeanFiltering (class in moonstone.filtering.taxonomy_filtering) TaxonomyNamesFiltering (class in moonstone.filtering.taxonomy_filtering) TaxonomyRandomSelection (class in moonstone.normalization.counts.random_selection) terms_to_remove (moonstone.parsers.counts.taxonomy.qiime.Qiime2Parser attribute) test_default() (moonstone.analysis.differential_analysis.DifferentialAnalysis method) test_dichotomic_features() (moonstone.analysis.differential_analysis.DifferentialAnalysis method) test_multiple_features() (moonstone.analysis.differential_analysis.DifferentialAnalysis method) tests_functions_used (moonstone.analysis.differential_analysis.DifferentialAnalysis attribute) TotalCountsNormalization (class in moonstone.normalization.counts.total_counts)

V

visualize() (moonstone.filtering.basics_filtering.NamesFiltering method) (moonstone.filtering.basics_filtering.NaNPercentageFiltering method) (moonstone.filtering.basics_filtering.NoCountsFiltering method) (moonstone.filtering.basics_filtering.NumberOfDifferentValuesFiltering method) (moonstone.filtering.mean_filtering.MeanFiltering method) (moonstone.filtering.taxonomy_filtering.TaxonomyMeanFiltering method) (moonstone.filtering.taxonomy_filtering.TaxonomyNamesFiltering method) (moonstone.normalization.counts.geometric_mean.GeometricMeanNormalization method) (moonstone.normalization.counts.random_selection.RandomSelection method) (moonstone.normalization.counts.random_selection.TaxonomyRandomSelection method) (moonstone.normalization.counts.total_counts.TotalCountsNormalization method)

visualize_categories() (moonstone.parsers.metadata.MetadataParser method)

Y

YAMLBasedMetadataParser (class in moonstone.parsers.metadata)