njab package

not just another biomarker (njab) - a package for biomarker discovery

Provides an opinionated workflow for biomarker discovery, using mimimum redundancy maximum relevance (MRMR) feature selection and logistic regression as a simple and explainable model.

Subpackages

• njab.io package
  • print_files()
• njab.pandas package
  • col_isin_df()
  • combine_value_counts()
  • get_colums_accessor()
  • get_overlapping_columns()
  • replace_with()
  • set_pandas_number_formatting()
  • set_pandas_options()
  • value_counts_with_margins()
• njab.plotting package
  • compare_km_curves()
  • plot_lifelines()
  • Submodules
    • njab.plotting.km module
      • compare_km_curves()
      • log_rank_test()
    • njab.plotting.lifelines module
      • plot_lifelines()
    • njab.plotting.metrics module
      • plot_auc()
      • plot_prc()
      • plot_split_auc()
      • plot_split_prc()
• njab.sklearn package
  • StandardScaler
    • StandardScaler.inverse_transform()
    • StandardScaler.set_fit_request()
    • StandardScaler.set_inverse_transform_request()
    • StandardScaler.set_partial_fit_request()
    • StandardScaler.set_transform_request()
    • StandardScaler.transform()
  • find_n_best_features()
  • get_results_split()
  • run_model()
  • run_pca()
  • Submodules
    • njab.sklearn.pca module
      • plot_explained_variance()
      • run_pca()
    • njab.sklearn.preprocessing module
      • StandardScaler
    • njab.sklearn.scoring module
      • ConfusionMatrix
      • get_custom_pred()
      • get_label_binary_classification()
      • get_lr_multiplicative_decomposition()
      • get_pred()
      • get_score()
      • get_target_count_per_bin()
    • njab.sklearn.types module
      • AucRocCurve
      • PrecisionRecallCurve
      • Results
      • ResultsSplit
      • Splits
• njab.stats package
  • binomtest()
  • diff_analysis()
  • Submodules
    • njab.stats.ancova module
      • Ancova
      • AncovaAll
      • AncovaOnlyTarget
      • add_fdr_scores()
      • ancova_pg()
      • filter_all_covars_from_scores()
      • filter_residuals_from_scores()
    • njab.stats.groups_comparision module
      • binomtest()
      • calc_stats()
      • diff_analysis()
      • means_between_groups()