Index

A

acore module acore.batch_correction module acore.correlation_analysis module acore.decomposition module acore.decomposition.pca module acore.decomposition.umap module acore.differential_regulation module acore.differential_regulation.format_test_table module acore.differential_regulation.tests module acore.drift_correction module acore.drift_correction.cpca_drift_correction module acore.drift_correction.loess_drift_correction module acore.enrichment_analysis module acore.enrichment_analysis.annotate module acore.enrichment_analysis.statistical_tests module acore.enrichment_analysis.statistical_tests.fisher module acore.enrichment_analysis.statistical_tests.kolmogorov_smirnov module acore.exploratory_analysis module acore.filter_metabolomics module acore.imputation_analysis module acore.io module acore.io.download module acore.io.ftp module acore.io.kegg module acore.io.pride module acore.io.uncompress module acore.io.uniprot module

acore.io.uniprot.uniprot module acore.kaplan_meier_analysis module acore.multiple_testing module acore.network_analysis module acore.normalization module acore.normalization.strategies module acore.power_analysis module acore.publications_analysis module acore.sklearn module acore.tda_analysis module acore.types module acore.types.differential_analysis module acore.types.enrichment_analysis module acore.types.exploratory_analysis module acore.utils module acore.wgcna_analysis module add_missing_columns (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) AncovaSchema (class in acore.types.differential_analysis) AncovaSchema.Config (class in acore.types.differential_analysis) angle_between() (in module acore.utils) annotate_features() (in module acore.enrichment_analysis.annotate) AnnotationResult (class in acore.types.exploratory_analysis) AnovaSchema (class in acore.types.differential_analysis) AnovaSchema.Config (class in acore.types.differential_analysis) AnovaSchemaMultiGroup (class in acore.types.differential_analysis) AnovaSchemaMultiGroup.Config (class in acore.types.differential_analysis) append_to_list() (in module acore.utils) apply_pvalue_correction() (in module acore.multiple_testing) apply_pvalue_fdrcorrection() (in module acore.multiple_testing) apply_pvalue_permutation_fdrcorrection() (in module acore.multiple_testing) apply_pvalue_twostage_fdrcorrection() (in module acore.multiple_testing)

B

background (EnrichmentAnalysisSchema attribute) background_pop (EnrichmentAnalysisSchema attribute) build_schema_() (AncovaSchema class method) (AnovaSchema class method) (AnovaSchemaMultiGroup class method) (EnrichmentAnalysisSchema class method) (TwoComponentSchema class method) (TwoLoadingsSchema class method)

build_schema_all_floats() (in module acore.types)

C

calc_means_between_groups() (in module acore.differential_regulation.tests) calc_ttest() (in module acore.differential_regulation.tests) calculate_ancova() (in module acore.differential_regulation.tests) calculate_anova() (in module acore.differential_regulation.tests) (in module acore.multiple_testing) calculate_coef_of_var_and_mean() (in module acore.exploratory_analysis) calculate_coefficient_variation() (in module acore.exploratory_analysis) calculate_correlations() (in module acore.correlation_analysis) calculate_fold_change() (in module acore.utils) calculate_mixed_anova() (in module acore.differential_regulation.tests) calculate_pairwise_ttest() (in module acore.differential_regulation.tests) calculate_pvalue_correlation() (in module acore.correlation_analysis) calculate_pvalue_correlation_old() (in module acore.correlation_analysis) calculate_pvalue_from_tstats() (in module acore.differential_regulation.tests) calculate_repeated_measures_anova() (in module acore.differential_regulation.tests) calculate_rm_correlation() (in module acore.correlation_analysis) calculate_thsd() (in module acore.differential_regulation.tests) calculate_ttest() (in module acore.differential_regulation.tests) check_id_mapping_results_ready() (in module acore.io.uniprot.uniprot) check_is_paired() (in module acore.utils) check_missingness() (in module acore.drift_correction) (in module acore.drift_correction.cpca_drift_correction) check_numeric_dataframe() (in module acore.types) check_response() (in module acore.io.uniprot.uniprot)

cid_to_kegg_id() (in module acore.io.kegg) coef (AncovaSchema attribute) coefficient (CorrelationCoefficient attribute) coerce (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) cohens_d() (in module acore.utils) combat_batch_correction() (in module acore.batch_correction) combine_batches() (in module acore.io.uniprot.uniprot) comparison (EnrichmentAnalysisSchema attribute) complement_posthoc() (in module acore.differential_regulation.tests) conf_int_low (AncovaSchema attribute) conf_int_upp (AncovaSchema attribute) convertToEdgeList() (in module acore.utils) corr_lower_triangle() (in module acore.correlation_analysis) correct_pairwise_ttest() (in module acore.multiple_testing) correction (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) CorrelationCoefficient (class in acore.correlation_analysis) count() (CorrelationCoefficient method) cpca_centroid() (in module acore.drift_correction) (in module acore.drift_correction.cpca_drift_correction)

D

decode_results() (in module acore.io.uniprot.uniprot) description (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) direction (EnrichmentAnalysisSchema attribute) download_file() (in module acore.io) (in module acore.io.download) download_from_ftp() (in module acore.io.ftp) download_PRIDE_data() (in module acore.io) (in module acore.io.pride)

drop_invalid_rows (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) dtype (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute)

E

efftype (AnovaSchemaMultiGroup attribute) empty() (AncovaSchema class method) (AnovaSchema class method) (AnovaSchemaMultiGroup class method) (EnrichmentAnalysisSchema class method) (TwoComponentSchema class method) (TwoLoadingsSchema class method) EnrichmentAnalysisSchema (class in acore.types.enrichment_analysis) EnrichmentAnalysisSchema.Config (class in acore.types.enrichment_analysis)

eta_squared() (in module acore.differential_regulation.tests) example() (AncovaSchema class method) (AnovaSchema class method) (AnovaSchemaMultiGroup class method) (EnrichmentAnalysisSchema class method) (TwoComponentSchema class method) (TwoLoadingsSchema class method) extract_number_missing() (in module acore.exploratory_analysis) extract_percentage_missing() (in module acore.exploratory_analysis)

F

f_statistics (AncovaSchema attribute) (AnovaSchemaMultiGroup attribute) FC (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) fetch_annotations() (in module acore.io.uniprot) fetch_kegg_ko_descriptions() (in module acore.io.kegg) filter_blanks() (in module acore.filter_metabolomics) filter_by_missingness() (in module acore.filter_metabolomics) filter_cv() (in module acore.filter_metabolomics) filter_features_by_qc() (in module acore.drift_correction.loess_drift_correction) flatten() (in module acore.utils) foreground (EnrichmentAnalysisSchema attribute) foreground_pop (EnrichmentAnalysisSchema attribute) format_anova_table() (in module acore.differential_regulation.tests) from_format (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute)

from_format_kwargs (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) from_json() (AncovaSchema class method) (AnovaSchema class method) (AnovaSchemaMultiGroup class method) (EnrichmentAnalysisSchema class method) (TwoComponentSchema class method) (TwoLoadingsSchema class method) from_yaml() (AncovaSchema class method) (AnovaSchema class method) (AnovaSchemaMultiGroup class method) (EnrichmentAnalysisSchema class method) (TwoComponentSchema class method) (TwoLoadingsSchema class method)

G

generator_to_dict() (in module acore.utils) get_batch() (in module acore.io.uniprot.uniprot) get_coefficient_variation() (in module acore.exploratory_analysis) get_counts_permutation_fdr() (in module acore.multiple_testing) get_data_ready_for_km() (in module acore.kaplan_meier_analysis) get_hazard_ratio_results() (in module acore.kaplan_meier_analysis) get_histogram_series() (in module acore.exploratory_analysis) get_id_mapping_results_link() (in module acore.io.uniprot.uniprot) get_id_mapping_results_search() (in module acore.io.uniprot.uniprot) get_id_mapping_results_stream() (in module acore.io.uniprot.uniprot) get_km_results() (in module acore.kaplan_meier_analysis) get_louvain_partitions() (in module acore.network_analysis) get_max_permutations() (in module acore.multiple_testing) get_metadata() (AncovaSchema class method) (AnovaSchema class method) (AnovaSchemaMultiGroup class method) (EnrichmentAnalysisSchema class method) (TwoComponentSchema class method) (TwoLoadingsSchema class method)

get_network_communities() (in module acore.network_analysis) get_next_link() (in module acore.io.uniprot.uniprot) get_publications_abstracts() (in module acore.publications_analysis) get_snf_clusters() (in module acore.network_analysis) get_xml_namespace() (in module acore.io.uniprot.uniprot) getMedlineAbstracts() (in module acore.publications_analysis) group (AnnotationResult attribute) (TwoComponentSchema attribute) (TwoLoadingsSchema attribute) group1 (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) group2 (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) group_data_based_on_marker() (in module acore.kaplan_meier_analysis)

H

hedges_g() (in module acore.utils)

I

identifiers (EnrichmentAnalysisSchema attribute) imputation_half_minimum() (in module acore.imputation_analysis) imputation_KNN() (in module acore.imputation_analysis)

imputation_mixed_norm_KNN() (in module acore.imputation_analysis) imputation_normal_distribution() (in module acore.imputation_analysis) imputation_zeros() (in module acore.imputation_analysis) index() (CorrelationCoefficient method)

L

linear_normalization() (in module acore.normalization.strategies) link_kegg_batch() (in module acore.io.kegg)

log2FC (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) lookup_cid_to_kegg_id() (in module acore.io.kegg)

M

mean_group1 (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) mean_group2 (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) median_normalization() (in module acore.normalization.strategies) median_polish_normalization() (in module acore.normalization.strategies) median_zero_normalization() (in module acore.normalization.strategies) merge_xml_results() (in module acore.io.uniprot.uniprot) metadata (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) Method (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) model_config (AnnotationResult attribute) module acore acore.batch_correction acore.correlation_analysis acore.decomposition acore.decomposition.pca acore.decomposition.umap acore.differential_regulation acore.differential_regulation.format_test_table acore.differential_regulation.tests acore.drift_correction acore.drift_correction.cpca_drift_correction acore.drift_correction.loess_drift_correction acore.enrichment_analysis acore.enrichment_analysis.annotate acore.enrichment_analysis.statistical_tests acore.enrichment_analysis.statistical_tests.fisher acore.enrichment_analysis.statistical_tests.kolmogorov_smirnov acore.exploratory_analysis acore.filter_metabolomics acore.imputation_analysis acore.io acore.io.download acore.io.ftp acore.io.kegg acore.io.pride acore.io.uncompress acore.io.uniprot acore.io.uniprot.uniprot acore.kaplan_meier_analysis acore.multiple_testing acore.network_analysis acore.normalization acore.normalization.strategies acore.power_analysis acore.publications_analysis acore.sklearn acore.tda_analysis acore.types acore.types.differential_analysis acore.types.enrichment_analysis acore.types.exploratory_analysis acore.utils acore.wgcna_analysis

most_central_edge() (in module acore.network_analysis) multiindex_coerce (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) multiindex_name (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) multiindex_ordered (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) multiindex_strict (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) multiindex_unique (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute)

N

name (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute)

neg_log10_p_value (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) normalize_data() (in module acore.normalization) normalize_data_per_group() (in module acore.normalization)

O

omega_squared() (in module acore.differential_regulation.tests) ordered (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute)

P

padj (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) (EnrichmentAnalysisSchema attribute) pairwise_ttest_with_covariates() (in module acore.differential_regulation.tests) parse_compound_pathway_mapping() (in module acore.io.kegg) parse_kegg_name_description() (in module acore.io.kegg) pooled_standard_deviation() (in module acore.utils) posthoc_BF10 (AnovaSchemaMultiGroup attribute) posthoc_dof (AnovaSchemaMultiGroup attribute) posthoc_effsize (AnovaSchemaMultiGroup attribute) posthoc_padj (AncovaSchema attribute) (AnovaSchemaMultiGroup attribute) posthoc_paired (AnovaSchemaMultiGroup attribute) posthoc_parametric (AnovaSchemaMultiGroup attribute) posthoc_pvalue (AncovaSchema attribute) (AnovaSchemaMultiGroup attribute)

posthoc_tail (AnovaSchemaMultiGroup attribute) power_analysis() (in module acore.power_analysis) print_progress_batches() (in module acore.io.uniprot.uniprot) process_annotations() (in module acore.io.uniprot) pvalue (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) (CorrelationCoefficient attribute) (EnrichmentAnalysisSchema attribute) pydantic_validate() (AncovaSchema class method) (AnovaSchema class method) (AnovaSchemaMultiGroup class method) (EnrichmentAnalysisSchema class method) (TwoComponentSchema class method) (TwoLoadingsSchema class method)

Q

qc_rlsc_loess() (in module acore.drift_correction) (in module acore.drift_correction.loess_drift_correction)

quantile_normalization() (in module acore.normalization.strategies)

R

rejected (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) (EnrichmentAnalysisSchema attribute) remove_group() (in module acore.utils) run_ancova() (in module acore.differential_regulation) run_anova() (in module acore.differential_regulation) run_correlation() (in module acore.correlation_analysis) run_cpca_drift_correction() (in module acore.drift_correction) (in module acore.drift_correction.cpca_drift_correction) run_diff_analysis() (in module acore.differential_regulation) run_efficient_correlation() (in module acore.correlation_analysis) run_fisher() (in module acore.enrichment_analysis) (in module acore.enrichment_analysis.statistical_tests.fisher) run_km() (in module acore.kaplan_meier_analysis) run_kolmogorov_smirnov() (in module acore.enrichment_analysis) (in module acore.enrichment_analysis.statistical_tests.kolmogorov_smirnov)

run_loess_drift_correction() (in module acore.drift_correction) (in module acore.drift_correction.loess_drift_correction) run_mapper() (in module acore.tda_analysis) run_mixed_anova() (in module acore.differential_regulation) run_multi_correlation() (in module acore.correlation_analysis) run_pca() (in module acore.decomposition.pca) (in module acore.exploratory_analysis) run_repeated_measurements_anova() (in module acore.differential_regulation) run_rm_correlation() (in module acore.correlation_analysis) run_site_regulation_enrichment() (in module acore.enrichment_analysis) run_snf() (in module acore.network_analysis) run_tsne() (in module acore.exploratory_analysis) run_ttest() (in module acore.differential_regulation) run_two_way_anova() (in module acore.differential_regulation) run_umap() (in module acore.decomposition.umap) (in module acore.exploratory_analysis) run_up_down_regulation_enrichment() (in module acore.enrichment_analysis)

S

select_numeric_columns() (in module acore.types) std_err (AncovaSchema attribute) std_group1 (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) std_group2 (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) strategy() (AncovaSchema class method) (AnovaSchema class method) (AnovaSchemaMultiGroup class method) (EnrichmentAnalysisSchema class method) (TwoComponentSchema class method) (TwoLoadingsSchema class method)

strict (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) submit_id_mapping() (in module acore.io.uniprot.uniprot)

T

t_statistics (AncovaSchema attribute) (AnovaSchema attribute) (AnovaSchemaMultiGroup attribute) terms (EnrichmentAnalysisSchema attribute) title (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) to_format (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) to_format_buffer (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) to_format_kwargs (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) to_json() (AncovaSchema class method) (AnovaSchema class method) (AnovaSchemaMultiGroup class method) (EnrichmentAnalysisSchema class method) (TwoComponentSchema class method) (TwoLoadingsSchema class method)

to_json_schema() (AncovaSchema class method) (AnovaSchema class method) (AnovaSchemaMultiGroup class method) (EnrichmentAnalysisSchema class method) (TwoComponentSchema class method) (TwoLoadingsSchema class method) to_schema() (AncovaSchema class method) (AnovaSchema class method) (AnovaSchemaMultiGroup class method) (EnrichmentAnalysisSchema class method) (TwoComponentSchema class method) (TwoLoadingsSchema class method) to_yaml() (AncovaSchema class method) (AnovaSchema class method) (AnovaSchemaMultiGroup class method) (EnrichmentAnalysisSchema class method) (TwoComponentSchema class method) (TwoLoadingsSchema class method) transform_DataFrame() (in module acore.sklearn) transform_into_long_format() (in module acore.utils) transform_into_wide_format() (in module acore.utils) TwoComponentSchema (class in acore.types.exploratory_analysis) TwoComponentSchema.Config (class in acore.types.exploratory_analysis) TwoLoadingsSchema (class in acore.types.exploratory_analysis) TwoLoadingsSchema.Config (class in acore.types.exploratory_analysis)

U

unique (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute) unique_column_names (AncovaSchema.Config attribute) (AnovaSchema.Config attribute) (AnovaSchemaMultiGroup.Config attribute) (EnrichmentAnalysisSchema.Config attribute) (TwoComponentSchema.Config attribute) (TwoLoadingsSchema.Config attribute)

unit_vector() (in module acore.utils) unrar() (in module acore.io) (in module acore.io.uncompress)

V

validate() (AncovaSchema class method) (AnovaSchema class method) (AnovaSchemaMultiGroup class method) (EnrichmentAnalysisSchema class method) (TwoComponentSchema class method) (TwoLoadingsSchema class method)

value (TwoLoadingsSchema attribute)

X

x (TwoComponentSchema attribute) (TwoLoadingsSchema attribute)

x_title (AnnotationResult attribute)

Y

y (TwoComponentSchema attribute) (TwoLoadingsSchema attribute)

y_title (AnnotationResult attribute)

Z

zscore_normalization() (in module acore.normalization.strategies)