# acore

* [acore package](acore.md)
  * [Subpackages](acore.md#subpackages)
    * [acore.batch_correction package](acore.batch_correction.md)
      * [`combat_batch_correction()`](acore.batch_correction.md#acore.batch_correction.combat_batch_correction)
    * [acore.correlation_analysis package](acore.correlation_analysis.md)
      * [`CorrelationCoefficient`](acore.correlation_analysis.md#acore.correlation_analysis.CorrelationCoefficient)
      * [`corr_lower_triangle()`](acore.correlation_analysis.md#acore.correlation_analysis.corr_lower_triangle)
      * [`calculate_correlations()`](acore.correlation_analysis.md#acore.correlation_analysis.calculate_correlations)
      * [`run_correlation()`](acore.correlation_analysis.md#acore.correlation_analysis.run_correlation)
      * [`run_multi_correlation()`](acore.correlation_analysis.md#acore.correlation_analysis.run_multi_correlation)
      * [`calculate_rm_correlation()`](acore.correlation_analysis.md#acore.correlation_analysis.calculate_rm_correlation)
      * [`run_rm_correlation()`](acore.correlation_analysis.md#acore.correlation_analysis.run_rm_correlation)
      * [`calculate_pvalue_correlation_old()`](acore.correlation_analysis.md#acore.correlation_analysis.calculate_pvalue_correlation_old)
      * [`calculate_pvalue_correlation()`](acore.correlation_analysis.md#acore.correlation_analysis.calculate_pvalue_correlation)
      * [`run_efficient_correlation()`](acore.correlation_analysis.md#acore.correlation_analysis.run_efficient_correlation)
    * [acore.decomposition package](acore.decomposition.md)
      * [Submodules](acore.decomposition.md#submodules)
      * [acore.decomposition.pca module](acore.decomposition.md#module-acore.decomposition.pca)
      * [acore.decomposition.umap module](acore.decomposition.md#module-acore.decomposition.umap)
    * [acore.differential_regulation package](acore.differential_regulation.md)
      * [`run_anova()`](acore.differential_regulation.md#acore.differential_regulation.run_anova)
      * [`run_ancova()`](acore.differential_regulation.md#acore.differential_regulation.run_ancova)
      * [`run_diff_analysis()`](acore.differential_regulation.md#acore.differential_regulation.run_diff_analysis)
      * [`run_mixed_anova()`](acore.differential_regulation.md#acore.differential_regulation.run_mixed_anova)
      * [`run_repeated_measurements_anova()`](acore.differential_regulation.md#acore.differential_regulation.run_repeated_measurements_anova)
      * [`run_ttest()`](acore.differential_regulation.md#acore.differential_regulation.run_ttest)
      * [`run_two_way_anova()`](acore.differential_regulation.md#acore.differential_regulation.run_two_way_anova)
      * [Submodules](acore.differential_regulation.md#submodules)
      * [acore.differential_regulation.format_test_table module](acore.differential_regulation.md#module-acore.differential_regulation.format_test_table)
      * [acore.differential_regulation.tests module](acore.differential_regulation.md#module-acore.differential_regulation.tests)
    * [acore.drift_correction package](acore.drift_correction.md)
      * [`check_missingness()`](acore.drift_correction.md#acore.drift_correction.check_missingness)
      * [`cpca_centroid()`](acore.drift_correction.md#acore.drift_correction.cpca_centroid)
      * [`run_cpca_drift_correction()`](acore.drift_correction.md#acore.drift_correction.run_cpca_drift_correction)
      * [`run_loess_drift_correction()`](acore.drift_correction.md#acore.drift_correction.run_loess_drift_correction)
      * [`qc_rlsc_loess()`](acore.drift_correction.md#acore.drift_correction.qc_rlsc_loess)
      * [Submodules](acore.drift_correction.md#submodules)
      * [acore.drift_correction.cpca_drift_correction module](acore.drift_correction.md#module-acore.drift_correction.cpca_drift_correction)
      * [acore.drift_correction.loess_drift_correction module](acore.drift_correction.md#module-acore.drift_correction.loess_drift_correction)
    * [acore.enrichment_analysis package](acore.enrichment_analysis.md)
      * [`run_site_regulation_enrichment()`](acore.enrichment_analysis.md#acore.enrichment_analysis.run_site_regulation_enrichment)
      * [`run_up_down_regulation_enrichment()`](acore.enrichment_analysis.md#acore.enrichment_analysis.run_up_down_regulation_enrichment)
      * [`run_fisher()`](acore.enrichment_analysis.md#acore.enrichment_analysis.run_fisher)
      * [`run_kolmogorov_smirnov()`](acore.enrichment_analysis.md#acore.enrichment_analysis.run_kolmogorov_smirnov)
      * [Subpackages](acore.enrichment_analysis.md#subpackages)
      * [Submodules](acore.enrichment_analysis.md#submodules)
      * [acore.enrichment_analysis.annotate module](acore.enrichment_analysis.md#module-acore.enrichment_analysis.annotate)
    * [acore.exploratory_analysis package](acore.exploratory_analysis.md)
      * [`get_histogram_series()`](acore.exploratory_analysis.md#acore.exploratory_analysis.get_histogram_series)
      * [`calculate_coefficient_variation()`](acore.exploratory_analysis.md#acore.exploratory_analysis.calculate_coefficient_variation)
      * [`calculate_coef_of_var_and_mean()`](acore.exploratory_analysis.md#acore.exploratory_analysis.calculate_coef_of_var_and_mean)
      * [`get_coefficient_variation()`](acore.exploratory_analysis.md#acore.exploratory_analysis.get_coefficient_variation)
      * [`extract_number_missing()`](acore.exploratory_analysis.md#acore.exploratory_analysis.extract_number_missing)
      * [`extract_percentage_missing()`](acore.exploratory_analysis.md#acore.exploratory_analysis.extract_percentage_missing)
      * [`run_pca()`](acore.exploratory_analysis.md#acore.exploratory_analysis.run_pca)
      * [`run_tsne()`](acore.exploratory_analysis.md#acore.exploratory_analysis.run_tsne)
      * [`run_umap()`](acore.exploratory_analysis.md#acore.exploratory_analysis.run_umap)
    * [acore.filter_metabolomics package](acore.filter_metabolomics.md)
      * [`filter_by_missingness()`](acore.filter_metabolomics.md#acore.filter_metabolomics.filter_by_missingness)
      * [`filter_cv()`](acore.filter_metabolomics.md#acore.filter_metabolomics.filter_cv)
      * [`filter_blanks()`](acore.filter_metabolomics.md#acore.filter_metabolomics.filter_blanks)
    * [acore.imputation_analysis package](acore.imputation_analysis.md)
      * [`imputation_KNN()`](acore.imputation_analysis.md#acore.imputation_analysis.imputation_KNN)
      * [`imputation_mixed_norm_KNN()`](acore.imputation_analysis.md#acore.imputation_analysis.imputation_mixed_norm_KNN)
      * [`imputation_normal_distribution()`](acore.imputation_analysis.md#acore.imputation_analysis.imputation_normal_distribution)
      * [`imputation_zeros()`](acore.imputation_analysis.md#acore.imputation_analysis.imputation_zeros)
      * [`imputation_half_minimum()`](acore.imputation_analysis.md#acore.imputation_analysis.imputation_half_minimum)
    * [acore.io package](acore.io.md)
      * [`download_PRIDE_data()`](acore.io.md#acore.io.download_PRIDE_data)
      * [`unrar()`](acore.io.md#acore.io.unrar)
      * [`download_file()`](acore.io.md#acore.io.download_file)
      * [Subpackages](acore.io.md#subpackages)
      * [Submodules](acore.io.md#submodules)
      * [acore.io.download module](acore.io.md#module-acore.io.download)
      * [acore.io.ftp module](acore.io.md#module-acore.io.ftp)
      * [acore.io.kegg module](acore.io.md#module-acore.io.kegg)
      * [acore.io.pride module](acore.io.md#module-acore.io.pride)
      * [acore.io.uncompress module](acore.io.md#module-acore.io.uncompress)
    * [acore.kaplan_meier_analysis package](acore.kaplan_meier_analysis.md)
      * [`get_data_ready_for_km()`](acore.kaplan_meier_analysis.md#acore.kaplan_meier_analysis.get_data_ready_for_km)
      * [`group_data_based_on_marker()`](acore.kaplan_meier_analysis.md#acore.kaplan_meier_analysis.group_data_based_on_marker)
      * [`run_km()`](acore.kaplan_meier_analysis.md#acore.kaplan_meier_analysis.run_km)
      * [`get_km_results()`](acore.kaplan_meier_analysis.md#acore.kaplan_meier_analysis.get_km_results)
      * [`get_hazard_ratio_results()`](acore.kaplan_meier_analysis.md#acore.kaplan_meier_analysis.get_hazard_ratio_results)
    * [acore.multiple_testing package](acore.multiple_testing.md)
      * [`apply_pvalue_correction()`](acore.multiple_testing.md#acore.multiple_testing.apply_pvalue_correction)
      * [`apply_pvalue_fdrcorrection()`](acore.multiple_testing.md#acore.multiple_testing.apply_pvalue_fdrcorrection)
      * [`apply_pvalue_twostage_fdrcorrection()`](acore.multiple_testing.md#acore.multiple_testing.apply_pvalue_twostage_fdrcorrection)
      * [`apply_pvalue_permutation_fdrcorrection()`](acore.multiple_testing.md#acore.multiple_testing.apply_pvalue_permutation_fdrcorrection)
      * [`calculate_anova()`](acore.multiple_testing.md#acore.multiple_testing.calculate_anova)
      * [`get_counts_permutation_fdr()`](acore.multiple_testing.md#acore.multiple_testing.get_counts_permutation_fdr)
      * [`get_max_permutations()`](acore.multiple_testing.md#acore.multiple_testing.get_max_permutations)
      * [`correct_pairwise_ttest()`](acore.multiple_testing.md#acore.multiple_testing.correct_pairwise_ttest)
    * [acore.network_analysis package](acore.network_analysis.md)
      * [`get_network_communities()`](acore.network_analysis.md#acore.network_analysis.get_network_communities)
      * [`get_snf_clusters()`](acore.network_analysis.md#acore.network_analysis.get_snf_clusters)
      * [`most_central_edge()`](acore.network_analysis.md#acore.network_analysis.most_central_edge)
      * [`get_louvain_partitions()`](acore.network_analysis.md#acore.network_analysis.get_louvain_partitions)
      * [`run_snf()`](acore.network_analysis.md#acore.network_analysis.run_snf)
    * [acore.normalization package](acore.normalization.md)
      * [`normalize_data()`](acore.normalization.md#acore.normalization.normalize_data)
      * [`normalize_data_per_group()`](acore.normalization.md#acore.normalization.normalize_data_per_group)
      * [Submodules](acore.normalization.md#submodules)
      * [acore.normalization.strategies module](acore.normalization.md#module-acore.normalization.strategies)
    * [acore.power_analysis package](acore.power_analysis.md)
      * [`power_analysis()`](acore.power_analysis.md#acore.power_analysis.power_analysis)
    * [acore.publications_analysis package](acore.publications_analysis.md)
      * [`getMedlineAbstracts()`](acore.publications_analysis.md#acore.publications_analysis.getMedlineAbstracts)
      * [`get_publications_abstracts()`](acore.publications_analysis.md#acore.publications_analysis.get_publications_abstracts)
    * [acore.sklearn package](acore.sklearn.md)
      * [`transform_DataFrame()`](acore.sklearn.md#acore.sklearn.transform_DataFrame)
    * [acore.tda_analysis package](acore.tda_analysis.md)
      * [`run_mapper()`](acore.tda_analysis.md#acore.tda_analysis.run_mapper)
    * [acore.types package](acore.types.md)
      * [`check_numeric_dataframe()`](acore.types.md#acore.types.check_numeric_dataframe)
      * [`select_numeric_columns()`](acore.types.md#acore.types.select_numeric_columns)
      * [`build_schema_all_floats()`](acore.types.md#acore.types.build_schema_all_floats)
      * [Submodules](acore.types.md#submodules)
      * [acore.types.differential_analysis module](acore.types.md#module-acore.types.differential_analysis)
      * [acore.types.enrichment_analysis module](acore.types.md#module-acore.types.enrichment_analysis)
      * [acore.types.exploratory_analysis module](acore.types.md#module-acore.types.exploratory_analysis)
  * [Submodules](acore.md#submodules)
  * [acore.utils module](acore.md#module-acore.utils)
    * [`convertToEdgeList()`](acore.md#acore.utils.convertToEdgeList)
    * [`check_is_paired()`](acore.md#acore.utils.check_is_paired)
    * [`transform_into_wide_format()`](acore.md#acore.utils.transform_into_wide_format)
    * [`transform_into_long_format()`](acore.md#acore.utils.transform_into_long_format)
    * [`remove_group()`](acore.md#acore.utils.remove_group)
    * [`calculate_fold_change()`](acore.md#acore.utils.calculate_fold_change)
    * [`pooled_standard_deviation()`](acore.md#acore.utils.pooled_standard_deviation)
    * [`cohens_d()`](acore.md#acore.utils.cohens_d)
    * [`hedges_g()`](acore.md#acore.utils.hedges_g)
    * [`unit_vector()`](acore.md#acore.utils.unit_vector)
    * [`flatten()`](acore.md#acore.utils.flatten)
    * [`angle_between()`](acore.md#acore.utils.angle_between)
    * [`append_to_list()`](acore.md#acore.utils.append_to_list)
    * [`generator_to_dict()`](acore.md#acore.utils.generator_to_dict)
  * [acore.wgcna_analysis module](acore.md#module-acore.wgcna_analysis)
