Thunor Core Modules Reference

These pages document the public modules and add a small amount of narrative context around the main entry points. For a package-level overview of how the pieces fit together, see Implementation notes.

• I/O, file reading and writing, core formats (thunor.io)
  • HtsPandas
    • HtsPandas.cell_lines
    • HtsPandas.drugs
    • HtsPandas.assay_names
    • HtsPandas.dip_assay_name
    • HtsPandas.doses_unstacked()
    • HtsPandas.filter()
    • HtsPandas.plate()
  • PlateData
  • PlateFileParseException
  • PlateMap
    • PlateMap.col_iterator()
    • PlateMap.num_wells
    • PlateMap.plate_size_from_num_wells()
    • PlateMap.row_iterator()
    • PlateMap.well_id_to_name()
    • PlateMap.well_iterator()
    • PlateMap.well_list()
    • PlateMap.well_name_to_id()
  • read_hdf()
  • read_incucyte()
  • read_vanderbilt_hts()
  • write_hdf()
  • write_vanderbilt_hts()
• DIP calculations and statistics (thunor.dip)
  • adjusted_r_squared()
  • ctrl_dip_rates()
  • dip_rates()
  • expt_dip_rates()
  • tyson1()
• Viability calculations and statistics (thunor.viability)
  • viability()
• Dose Response Curve Fitting (thunor.curve_fit)
  • AAFitWarning
  • AUCFitWarning
  • DrugCombosWarning
  • HillCurve
    • HillCurve.null_response_fn()
  • HillCurveLL2
    • HillCurveLL2.fit_fn()
    • HillCurveLL2.fit_fn_log()
    • HillCurveLL2.initial_guess()
    • HillCurveLL2.initial_guess_log()
    • HillCurveLL2.jac_fn_log()
    • HillCurveLL2.transform_popt_from_log()
    • HillCurveLL2.undo_dose_scale()
  • HillCurveLL3u
    • HillCurveLL3u.fit_fn()
    • HillCurveLL3u.fit_fn_log()
    • HillCurveLL3u.initial_guess()
    • HillCurveLL3u.initial_guess_log()
    • HillCurveLL3u.jac_fn_log()
    • HillCurveLL3u.max_fit_evals
    • HillCurveLL3u.null_response_fn()
    • HillCurveLL3u.transform_popt_from_log()
    • HillCurveLL3u.undo_dose_scale()
  • HillCurveLL4
    • HillCurveLL4.aa()
    • HillCurveLL4.auc()
    • HillCurveLL4.ec()
    • HillCurveLL4.fit_fn()
    • HillCurveLL4.fit_fn_log()
    • HillCurveLL4.ic()
    • HillCurveLL4.initial_guess()
    • HillCurveLL4.initial_guess_log()
    • HillCurveLL4.jac_fn_log()
    • HillCurveLL4.transform_popt_from_log()
    • HillCurveLL4.undo_dose_scale()
  • HillCurveNull
  • ValueWarning
  • aa_obs()
  • fit_drc()
  • fit_params()
  • fit_params_from_base()
  • fit_params_minimal()
  • is_param_truncated()
• Plots and visualisation (thunor.plots)
  • CannotPlotError
  • plot_ctrl_cell_counts_by_plate()
  • plot_ctrl_dip_by_plate()
  • plot_drc()
  • plot_drc_params()
  • plot_drug_combination_heatmap()
  • plot_plate_map()
  • plot_time_course()
  • plot_two_dataset_param_scatter()
• Miscellaneous “helper” functions (thunor.helpers)
  • format_dose()
  • plotly_to_dataframe()
• Conversion tools for external formats and databases (thunor.converters)
  • convert_ctrp()
  • convert_gdsc()
  • convert_gdsc_tags()
  • convert_teicher()