moonstone
stable
Moonstone
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User guide
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Getting started with moonstone
Available classes
Contribution guide
Contributing to Moonstone
API Documentation
Parsers
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Changelogs
Changelogs
moonstone
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Index
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C
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D
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F
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G
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L
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M
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N
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P
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Q
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R
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S
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Y
_
__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)