pyrnaither package

Subpackages

• pyrnaither.data package
  • Submodules
    • pyrnaither.data.datasets module
      • generate_dataset_file()
  • Module contents
• pyrnaither.logging package
  • Submodules
    • pyrnaither.logging.logger module
      • ColorFormatter
      • handle_exception()
      • setup_logger()
  • Module contents
• pyrnaither.normalization package
  • Submodules
    • pyrnaither.normalization.normalizer module
      • b_score()
      • control_norm()
      • div_norm()
      • lowess_norm()
      • med_abs_dev()
      • median_polish()
      • quantile_normalization()
      • save_dataset()
      • save_old_intensity_columns()
      • subtract_background()
      • var_adjust()
      • z_score()
      • z_score_per_screen()
  • Module contents
• pyrnaither.pipeline package
  • Submodules
    • pyrnaither.pipeline.workflow module
  • Module contents
• pyrnaither.stats package
  • Submodules
    • pyrnaither.stats.qc module
      • compare_replica_plates()
      • compare_replicate_sd()
      • compare_replicate_sd_per_screen()
      • compare_replicates()
      • control_density()
      • control_density_per_plate()
      • control_density_per_screen()
      • discard_labtek()
      • discard_wells()
      • dr_qual_control()
      • dynamic_range()
      • make_boxplot_4_plate_type()
      • make_boxplot_controls()
      • make_boxplot_controls_per_plate()
      • make_boxplot_controls_per_screen()
      • make_boxplot_per_plate()
      • make_boxplot_per_screen()
      • num_cell_qual_control()
      • perc_cell_qual_control()
      • plot_control_histo()
      • plot_control_histo_per_plate()
      • plot_histo()
      • plot_histo_per_plate()
      • plot_histo_per_screen()
      • plot_qq()
      • plot_qq_per_plate()
      • plot_qq_per_screen()
      • read_dataset_with_header()
      • replicates_cv()
      • replicates_spearman_cor()
      • snr_qual_control()
      • spatial_distrib()
      • z_prime()
      • zprime_qual_control()
    • pyrnaither.stats.qc_todo module
      • PdfPages()
      • generate_replicate_matrix()
      • summarize_reps_no_filtering()
    • pyrnaither.stats.stattests module
      • compare_hits()
      • hit_selection_pval()
      • hit_selection_zscore()
      • hit_selection_zscore_pval()
      • incorporate_pval_vec()
      • mann_whitney()
      • mult_test_adjust()
      • rank_product()
      • spatial_distrib_hits()
      • t_test()
      • venn_diag()
      • volcano_plot()
    • pyrnaither.stats.stattests_todo module
      • order_gene_ids()
  • Module contents
• pyrnaither.utils package
  • Submodules
    • pyrnaither.utils.utilities module
      • closest_to_zero()
      • create_subset()
      • divide_channels()
      • erase_dataset_column()
      • find_replicates()
      • furthest_from_zero()
      • generate_replicate_mat()
      • generate_replicate_matrix_no_filter()
      • index_subset()
      • order_gene_ids()
      • rms()
      • sum_channels()
      • summarize_reps()
      • trim_avg()
  • Module contents
• pyrnaither.visualization package
  • Submodules
    • pyrnaither.visualization.visualizer module
      • get_complementary_color()
      • plot_96_well_plate_with_intensity()
      • spatial_distrib()
  • Module contents

Submodules

• pyrnaither.main module
  • PyRNAither
    • PyRNAither.__init__()
    • PyRNAither.load_data()
    • PyRNAither.normalize()
    • PyRNAither.run_quality_control()
    • PyRNAither.visualize()
  • main()
  • parse_arguments()

Module contents

pyRNAither - A Python package for RNAi data analysis