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.parsers.counts.GeneCountsParser method) (moonstone.parsers.counts.Picrust2PathwaysParser method) (moonstone.parsers.counts.taxonomy.Metaphlan2Parser method) (moonstone.parsers.counts.taxonomy.Metaphlan3Parser method) (moonstone.parsers.counts.taxonomy.Qiime2Parser method) (moonstone.parsers.counts.taxonomy.SunbeamKraken2Parser 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)

C

calculating_and_substracting_mean_row() (moonstone.normalization.counts.geometric_mean.GeometricMeanNormalization 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)

D

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) 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)

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) Metaphlan3Parser (class in moonstone.parsers.counts.taxonomy) module 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.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

N

NamesFiltering (class in moonstone.filtering.basics_filtering) NaNPercentageFiltering (class in moonstone.filtering.basics_filtering) 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) NumberOfDifferentValuesFiltering (class in moonstone.filtering.basics_filtering)

P

Picrust2PathwaysParser (class in moonstone.parsers.counts) plot_age() (moonstone.plot.metadata.PlotMetadataStats method) plot_category_distribution() (moonstone.plot.metadata.PlotMetadataStats method) 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) prevalence_series() (moonstone.plot.counts.PlotTaxonomyCounts property)

Q

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

R

RandomSelection (class in moonstone.normalization.counts.random_selection) relative_abundance_dataframe() (moonstone.plot.counts.PlotTaxonomyCounts property) 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)

S

scaling_factors() (moonstone.normalization.counts.geometric_mean.GeometricMeanNormalization property) (moonstone.normalization.counts.total_counts.TotalCountsNormalization property)

SunbeamKraken2Parser (class in moonstone.parsers.counts.taxonomy)

T

TaxonomyMeanFiltering (class in moonstone.filtering.taxonomy_filtering) TaxonomyNamesFiltering (class in moonstone.filtering.taxonomy_filtering)

TaxonomyRandomSelection (class in moonstone.normalization.counts.random_selection) 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)

Y

YAMLBasedMetadataParser (class in moonstone.parsers.metadata)