Index

A

adjust_p_values() (in module cytepool.stats.multiple_testing) assign (cytepool.design.Design property)

attributes (cytepool.io.zarr.ZarrArray property) average_log_cpm() (in module cytepool.stats.quasi_likelihood)

B

beta_cdf() (in module cytepool.stats.distributions) beta_sf() (in module cytepool.stats.distributions)

betainc() (in module cytepool.stats.special) betaincc() (in module cytepool.stats.special)

C

camera() (in module cytepool.stats.gene_set_tests) check() (cytepool.design.Design method) check_compression() (in module cytepool.io.zarr) chi2_cdf() (in module cytepool.stats.distributions) chi2_isf() (in module cytepool.stats.distributions) chi2_logsf() (in module cytepool.stats.distributions) chi2_ppf() (in module cytepool.stats.distributions) chi2_sf() (in module cytepool.stats.distributions) choose_lowess_span() (in module cytepool.stats.smoothing) chunks (cytepool.io.zarr.ZarrArray property) coefficient_names (cytepool.stats.quasi_likelihood.QuasiLikelihoodFit property) collapse_samples() (cytepool.cube.Cube method) columns (cytepool.design.Design property) (cytepool.table.Table property) common_dispersion() (in module cytepool.stats.quasi_likelihood) CompositionResult (class in cytepool.composition) Contrasts (class in cytepool.design) contrasts (cytepool.composition.CompositionResult property) (cytepool.design.Design property) (cytepool.differential_expression.DifferentialExpressionResult property) contrasts_fit() (in module cytepool.stats.linear_models) cpm() (in module cytepool.normalization) Cube (class in cytepool.cube) cytepool.composition module cytepool.cube module cytepool.cube.fingerprints module cytepool.cube.provenance module cytepool.design module cytepool.differential_expression module cytepool.gene_sets module cytepool.io module cytepool.io.anndata module cytepool.io.zarr module

cytepool.meta_analysis module cytepool.normalization module cytepool.over_representation module cytepool.plotting module cytepool.stats.deseq2 module cytepool.stats.distributions module cytepool.stats.dream module cytepool.stats.empirical_bayes module cytepool.stats.gene_set_tests module cytepool.stats.linear_models module cytepool.stats.mixed_models module cytepool.stats.multiple_testing module cytepool.stats.negative_binomial_models module cytepool.stats.quasi_likelihood module cytepool.stats.rotation_gene_set_tests module cytepool.stats.sample_weights module cytepool.stats.smoothing module cytepool.stats.special module cytepool.stats.voom module cytepool.table module cytepool.variance_partitioning module

D

DATA_TYPES (in module cytepool.io.zarr) DEFAULT_LEVELS (in module cytepool.io.zarr) describe_provenance() (in module cytepool.cube.provenance) descriptions (cytepool.gene_sets.GeneSets property) deseq2_dispersions() (in module cytepool.stats.deseq2) deseq2_likelihood_ratio_test() (in module cytepool.stats.deseq2) deseq2_wald_test() (in module cytepool.stats.deseq2) DESeq2Dispersions (class in cytepool.stats.deseq2) DESeq2Fit (class in cytepool.stats.deseq2) DESeq2Results (class in cytepool.stats.deseq2)

Design (class in cytepool.design) DesignIssue (class in cytepool.design) DesignReport (class in cytepool.design) differential_expression_meta_analysis() (in module cytepool.meta_analysis) DifferentialExpressionResult (class in cytepool.differential_expression) digamma() (in module cytepool.stats.special) digests() (cytepool.cube.Cube method) dimension_names (cytepool.io.zarr.ZarrArray property) dream_voom() (in module cytepool.differential_expression) dtype (cytepool.io.zarr.ZarrArray property)

E

equals() (cytepool.table.Table method)

F

f_cdf() (in module cytepool.stats.distributions) f_isf() (in module cytepool.stats.distributions) f_logsf() (in module cytepool.stats.distributions) f_ppf() (in module cytepool.stats.distributions) f_sf() (in module cytepool.stats.distributions) f_test (cytepool.composition.CompositionResult property) f_tests (cytepool.differential_expression.DifferentialExpressionResult property) FDistributionFit (class in cytepool.stats.empirical_bayes) features (cytepool.cube.Cube property) file (cytepool.gene_sets.GeneSets property) fill_value (cytepool.io.zarr.ZarrArray property) filter() (cytepool.table.Table method) filter_by_expression() (in module cytepool.normalization) filter_by_size() (cytepool.gene_sets.GeneSets method) fingerprint() (cytepool.cube.Cube method) FINGERPRINT_VERSION (in module cytepool.cube.fingerprints) fit_deseq2() (in module cytepool.stats.deseq2) fit_f_distribution() (in module cytepool.stats.empirical_bayes)

fit_f_distribution_likelihood() (in module cytepool.stats.empirical_bayes) fit_f_distribution_robust() (in module cytepool.stats.empirical_bayes) fit_linear_model() (in module cytepool.stats.linear_models) fit_mixed_model() (in module cytepool.stats.mixed_models) fit_negative_binomial_model() (in module cytepool.stats.negative_binomial_models) fit_quasi_likelihood() (in module cytepool.stats.quasi_likelihood) fixed_effect_f_test() (in module cytepool.stats.mixed_models) fixed_effect_tests() (in module cytepool.stats.mixed_models) FixedEffectFTest (class in cytepool.stats.mixed_models) FixedEffectTests (class in cytepool.stats.mixed_models) formula (cytepool.design.Design property) FormulaTerms (class in cytepool.design) fraction_detected() (cytepool.cube.Cube method) from_anndata() (in module cytepool.io.anndata) from_bulk() (in module cytepool.cube) from_cells() (in module cytepool.cube) from_mudata() (in module cytepool.io.anndata) fry() (in module cytepool.stats.gene_set_tests)

G

gamma_cdf() (in module cytepool.stats.distributions) gamma_sf() (in module cytepool.stats.distributions) gammainc() (in module cytepool.stats.special) gammaincc() (in module cytepool.stats.special) GeneSets (class in cytepool.gene_sets)

get() (cytepool.design.Contrasts method) group (cytepool.design.RandomEffect property) groups (cytepool.cube.Cube property) (cytepool.differential_expression.DifferentialExpressionResult property) (cytepool.variance_partitioning.VariancePartitioningResult property)

H

history() (cytepool.cube.Cube method)

hypergeom_logsf() (in module cytepool.stats.distributions) hypergeom_sf() (in module cytepool.stats.distributions)

I

INTERCEPT (in module cytepool.design)

items() (cytepool.design.Contrasts method)

K

keys() (cytepool.design.Contrasts method)

kinds() (cytepool.design.DesignReport method)

L

labels (cytepool.design.FormulaTerms property) layer() (cytepool.cube.Cube method) layer_names (cytepool.cube.Cube property) levels (cytepool.design.Design property) lgamma() (in module cytepool.stats.special) library_sizes() (cytepool.cube.Cube method) (in module cytepool.normalization) licence (cytepool.gene_sets.GeneSets property) LikelihoodFDistributionFit (class in cytepool.stats.empirical_bayes)

limma_trend() (in module cytepool.differential_expression) limma_voom() (in module cytepool.differential_expression) LinearModelFit (class in cytepool.stats.linear_models) log_beta() (in module cytepool.stats.special) log_betainc() (in module cytepool.stats.special) log_betaincc() (in module cytepool.stats.special) log_cpm() (in module cytepool.normalization) log_gammainc() (in module cytepool.stats.special) log_gammaincc() (in module cytepool.stats.special) lowess() (in module cytepool.stats.smoothing)

M

make_contrasts() (in module cytepool.design) matrix (cytepool.design.Design property) MAX_CHUNK_BYTES (in module cytepool.io.zarr) mean() (cytepool.cube.Cube method) median_ratio_size_factors() (in module cytepool.normalization) meta_analysis() (in module cytepool.meta_analysis) MetaAnalysisFit (class in cytepool.meta_analysis) MetaAnalysisResult (class in cytepool.meta_analysis) METADATA_FILE (in module cytepool.io.zarr) method (cytepool.differential_expression.DifferentialExpressionResult property) MixedModelFit (class in cytepool.stats.mixed_models) model_matrix (cytepool.design.Design property) model_matrix() (in module cytepool.design) ModelMatrix (class in cytepool.design) moderated_fixed_effect_tests() (in module cytepool.stats.dream) moderated_statistics() (in module cytepool.stats.empirical_bayes) ModeratedFit (class in cytepool.stats.empirical_bayes) ModeratedFixedEffectTests (class in cytepool.stats.dream) module cytepool.composition cytepool.cube cytepool.cube.fingerprints cytepool.cube.provenance cytepool.design cytepool.differential_expression cytepool.gene_sets cytepool.io cytepool.io.anndata cytepool.io.zarr cytepool.meta_analysis cytepool.normalization cytepool.over_representation cytepool.plotting cytepool.stats.deseq2 cytepool.stats.distributions cytepool.stats.dream cytepool.stats.empirical_bayes cytepool.stats.gene_set_tests cytepool.stats.linear_models cytepool.stats.mixed_models cytepool.stats.multiple_testing cytepool.stats.negative_binomial_models cytepool.stats.quasi_likelihood cytepool.stats.rotation_gene_set_tests cytepool.stats.sample_weights cytepool.stats.smoothing cytepool.stats.special cytepool.stats.voom cytepool.table cytepool.variance_partitioning

mroast() (in module cytepool.stats.rotation_gene_set_tests)

N

n_cells (cytepool.cube.Cube property) n_features (cytepool.cube.Cube property) n_groups (cytepool.cube.Cube property) n_samples (cytepool.cube.Cube property) (cytepool.design.Design property) natural_spline_basis() (in module cytepool.stats.smoothing) ndim (cytepool.io.zarr.ZarrArray property) negative_binomial_deviance() (in module cytepool.stats.negative_binomial_models) negative_binomial_unit_deviance() (in module cytepool.stats.negative_binomial_models)

negative_binomial_unit_deviance_moments() (in module cytepool.stats.quasi_likelihood) NegativeBinomialFit (class in cytepool.stats.negative_binomial_models) norm_cdf() (in module cytepool.stats.distributions) norm_isf() (in module cytepool.stats.distributions) norm_logcdf() (in module cytepool.stats.distributions) norm_logsf() (in module cytepool.stats.distributions) norm_ppf() (in module cytepool.stats.distributions) norm_sf() (in module cytepool.stats.distributions) normalization (cytepool.cube.Cube property)

O

oindex (cytepool.io.zarr.ZarrArray property) ok (cytepool.design.DesignReport property)

open_array() (in module cytepool.io.zarr) over_representation() (in module cytepool.over_representation)

P

parse_formula() (in module cytepool.design) parse_random_effects() (in module cytepool.design) path (cytepool.io.zarr.ZarrArray property) plot_barcode() (in module cytepool.plotting) plot_cell_numbers() (in module cytepool.plotting) plot_composition() (in module cytepool.plotting) plot_dispersions() (in module cytepool.plotting) plot_forest() (in module cytepool.plotting) plot_gene_sets() (in module cytepool.plotting) plot_gene_variance_fractions() (in module cytepool.plotting) plot_md() (in module cytepool.plotting) plot_mds() (in module cytepool.plotting) plot_mean_variance() (in module cytepool.plotting) plot_over_representation() (in module cytepool.plotting)

plot_p_values() (in module cytepool.plotting) plot_proportions() (in module cytepool.plotting) plot_quasi_dispersions() (in module cytepool.plotting) plot_residual_variances() (in module cytepool.plotting) plot_sample_weights() (in module cytepool.plotting) plot_significant_genes() (in module cytepool.plotting) plot_variance_fractions() (in module cytepool.plotting) plot_volcano() (in module cytepool.plotting) propeller() (in module cytepool.composition) proportions (cytepool.composition.CompositionResult property) provenance (cytepool.composition.CompositionResult property) (cytepool.cube.Cube property) (cytepool.differential_expression.DifferentialExpressionResult property) (cytepool.meta_analysis.MetaAnalysisResult property) (cytepool.variance_partitioning.VariancePartitioningResult property)

Q

quasi_likelihood_f_test() (in module cytepool.stats.quasi_likelihood) QuasiLikelihoodFit (class in cytepool.stats.quasi_likelihood)

QuasiLikelihoodTest (class in cytepool.stats.quasi_likelihood) quote_name() (in module cytepool.design.formula)

R

random (cytepool.design.Design property) RandomEffect (class in cytepool.design) read_cube() (in module cytepool.io) read_gmt() (in module cytepool.gene_sets) read_group_attributes() (in module cytepool.io.zarr) regroup() (cytepool.cube.Cube method)

rename() (cytepool.table.Table method) residual_df (cytepool.design.DesignReport property) restrict_to() (cytepool.gene_sets.GeneSets method) rle_factors() (in module cytepool.normalization) roast() (in module cytepool.stats.rotation_gene_set_tests) RobustFDistributionFit (class in cytepool.stats.empirical_bayes) romer() (in module cytepool.stats.rotation_gene_set_tests)

S

sample_quality_weights() (in module cytepool.stats.sample_weights) samples (cytepool.composition.CompositionResult property) (cytepool.cube.Cube property) (cytepool.design.Design property) (cytepool.differential_expression.DifferentialExpressionResult property) (cytepool.variance_partitioning.VariancePartitioningResult property) select() (cytepool.cube.Cube method) (cytepool.design.Contrasts method) (cytepool.gene_sets.GeneSets method) (cytepool.table.Table method) settings (cytepool.composition.CompositionResult property) (cytepool.differential_expression.DifferentialExpressionResult property) (cytepool.meta_analysis.MetaAnalysisResult property) (cytepool.variance_partitioning.VariancePartitioningResult property)

sha256 (cytepool.gene_sets.GeneSets property) shape (cytepool.design.ModelMatrix property) (cytepool.io.zarr.ZarrArray property) source (cytepool.gene_sets.GeneSets property) squeeze_variances() (in module cytepool.stats.empirical_bayes) SqueezedVariances (class in cytepool.stats.empirical_bayes) studies (cytepool.meta_analysis.MetaAnalysisResult property) summary (cytepool.composition.CompositionResult property) (cytepool.differential_expression.DifferentialExpressionResult property) (cytepool.meta_analysis.MetaAnalysisResult property) (cytepool.variance_partitioning.VariancePartitioningResult property)

T

t_cdf() (in module cytepool.stats.distributions) t_isf() (in module cytepool.stats.distributions) t_logsf() (in module cytepool.stats.distributions) t_ppf() (in module cytepool.stats.distributions) t_sf() (in module cytepool.stats.distributions) Table (class in cytepool.table) table() (cytepool.composition.CompositionResult method) (cytepool.differential_expression.DifferentialExpressionResult method) (cytepool.meta_analysis.MetaAnalysisResult method) (cytepool.variance_partitioning.VariancePartitioningResult method) tables (cytepool.composition.CompositionResult property) (cytepool.differential_expression.DifferentialExpressionResult property) (cytepool.meta_analysis.MetaAnalysisResult property) (cytepool.variance_partitioning.VariancePartitioningResult property)

take() (cytepool.table.Table method) terms (cytepool.design.Design property) tmm_factors() (in module cytepool.normalization) to_anndata() (in module cytepool.io.anndata) to_dict() (cytepool.table.Table method) to_memory() (cytepool.cube.Cube method) to_mudata() (in module cytepool.io.anndata) to_pandas() (cytepool.table.Table method) treat() (in module cytepool.stats.empirical_bayes) TreatFit (class in cytepool.stats.empirical_bayes) trigamma() (in module cytepool.stats.special) trigamma_inverse() (in module cytepool.stats.special)

U

UnitDevianceMoments (class in cytepool.stats.quasi_likelihood)

upper_quartile_factors() (in module cytepool.normalization) used_variables (cytepool.design.FormulaTerms property)

V

values() (cytepool.design.Contrasts method) variables (cytepool.variance_partitioning.VariancePartitioningResult property) variance() (cytepool.cube.Cube method) variance_fractions() (in module cytepool.variance_partitioning) variance_partitioning() (in module cytepool.variance_partitioning) VarianceFractions (class in cytepool.variance_partitioning)

VariancePartitioningResult (class in cytepool.variance_partitioning) verify_fingerprint() (cytepool.cube.Cube method) version (cytepool.gene_sets.GeneSets property) voom() (in module cytepool.stats.voom) voom_with_dream_weights() (in module cytepool.stats.dream) voom_with_quality_weights() (in module cytepool.stats.voom) VoomResult (class in cytepool.stats.voom)

W

with_columns() (cytepool.table.Table method) with_contrasts() (cytepool.design.Design method) write_array() (in module cytepool.io.zarr)

write_cube() (in module cytepool.io) write_gmt() (in module cytepool.gene_sets) write_group() (in module cytepool.io.zarr)

Z

ZarrArray (class in cytepool.io.zarr)