acore package

Subpackages

• acore.batch_correction package
  • combat_batch_correction()
• acore.correlation_analysis package
  • CorrelationCoefficient
    • CorrelationCoefficient.coefficient
    • CorrelationCoefficient.pvalue
    • CorrelationCoefficient.count()
    • CorrelationCoefficient.index()
  • corr_lower_triangle()
  • calculate_correlations()
  • run_correlation()
  • run_multi_correlation()
  • calculate_rm_correlation()
  • run_rm_correlation()
  • calculate_pvalue_correlation_old()
  • calculate_pvalue_correlation()
  • run_efficient_correlation()
• acore.decomposition package
  • Submodules
    • acore.decomposition.pca module
      • run_pca()
    • acore.decomposition.umap module
      • run_umap()
• acore.differential_regulation package
  • run_anova()
  • run_ancova()
  • run_diff_analysis()
  • run_mixed_anova()
  • run_repeated_measurements_anova()
  • run_ttest()
  • run_two_way_anova()
  • Submodules
    • acore.differential_regulation.format_test_table module
    • acore.differential_regulation.tests module
      • calc_means_between_groups()
      • calc_ttest()
      • calculate_ttest()
      • calculate_thsd()
      • calculate_pairwise_ttest()
      • complement_posthoc()
      • calculate_anova()
      • calculate_ancova()
      • calculate_repeated_measures_anova()
      • calculate_mixed_anova()
      • pairwise_ttest_with_covariates()
      • format_anova_table()
      • calculate_pvalue_from_tstats()
      • eta_squared()
      • omega_squared()
• acore.drift_correction package
  • check_missingness()
  • cpca_centroid()
  • run_cpca_drift_correction()
  • run_loess_drift_correction()
  • qc_rlsc_loess()
  • Submodules
    • acore.drift_correction.cpca_drift_correction module
      • check_missingness()
      • run_cpca_drift_correction()
      • cpca_centroid()
    • acore.drift_correction.loess_drift_correction module
      • filter_features_by_qc()
      • qc_rlsc_loess()
      • run_loess_drift_correction()
• acore.enrichment_analysis package
  • run_site_regulation_enrichment()
  • run_up_down_regulation_enrichment()
  • run_fisher()
  • run_kolmogorov_smirnov()
  • Subpackages
    • acore.enrichment_analysis.statistical_tests namespace
      • Submodules
  • Submodules
    • acore.enrichment_analysis.annotate module
      • annotate_features()
• acore.exploratory_analysis package
  • get_histogram_series()
  • calculate_coefficient_variation()
  • calculate_coef_of_var_and_mean()
  • get_coefficient_variation()
  • extract_number_missing()
  • extract_percentage_missing()
  • run_pca()
  • run_tsne()
  • run_umap()
• acore.filter_metabolomics package
  • filter_by_missingness()
  • filter_cv()
  • filter_blanks()
• acore.imputation_analysis package
  • imputation_KNN()
  • imputation_mixed_norm_KNN()
  • imputation_normal_distribution()
  • imputation_zeros()
  • imputation_half_minimum()
• acore.io package
  • download_PRIDE_data()
  • unrar()
  • download_file()
  • Subpackages
    • acore.io.uniprot package
      • fetch_annotations()
      • process_annotations()
      • Submodules
  • Submodules
    • acore.io.download module
      • download_file()
    • acore.io.ftp module
      • download_from_ftp()
    • acore.io.kegg module
      • link_kegg_batch()
      • fetch_kegg_ko_descriptions()
      • cid_to_kegg_id()
      • parse_compound_pathway_mapping()
      • parse_kegg_name_description()
      • lookup_cid_to_kegg_id()
    • acore.io.pride module
      • download_PRIDE_data()
    • acore.io.uncompress module
      • unrar()
• acore.kaplan_meier_analysis package
  • get_data_ready_for_km()
  • group_data_based_on_marker()
  • run_km()
  • get_km_results()
  • get_hazard_ratio_results()
• acore.multiple_testing package
  • apply_pvalue_correction()
  • apply_pvalue_fdrcorrection()
  • apply_pvalue_twostage_fdrcorrection()
  • apply_pvalue_permutation_fdrcorrection()
  • calculate_anova()
  • get_counts_permutation_fdr()
  • get_max_permutations()
  • correct_pairwise_ttest()
• acore.network_analysis package
  • get_network_communities()
  • get_snf_clusters()
  • most_central_edge()
  • get_louvain_partitions()
  • run_snf()
• acore.normalization package
  • normalize_data()
  • normalize_data_per_group()
  • Submodules
    • acore.normalization.strategies module
      • median_zero_normalization()
      • median_normalization()
      • zscore_normalization()
      • median_polish_normalization()
      • quantile_normalization()
      • linear_normalization()
• acore.power_analysis package
  • power_analysis()
• acore.publications_analysis package
  • getMedlineAbstracts()
  • get_publications_abstracts()
• acore.sklearn package
  • transform_DataFrame()
• acore.tda_analysis package
  • run_mapper()
• acore.types package
  • check_numeric_dataframe()
  • select_numeric_columns()
  • build_schema_all_floats()
  • Submodules
    • acore.types.differential_analysis module
      • AnovaSchema
      • AnovaSchemaMultiGroup
      • AncovaSchema
    • acore.types.enrichment_analysis module
      • EnrichmentAnalysisSchema
    • acore.types.exploratory_analysis module
      • TwoComponentSchema
      • TwoLoadingsSchema
      • AnnotationResult

Submodules

• acore.utils module
  • convertToEdgeList()
  • check_is_paired()
  • transform_into_wide_format()
  • transform_into_long_format()
  • remove_group()
  • calculate_fold_change()
  • pooled_standard_deviation()
  • cohens_d()
  • hedges_g()
  • unit_vector()
  • flatten()
  • angle_between()
  • append_to_list()
  • generator_to_dict()
• acore.wgcna_analysis module