Dose Response Curve Evaluation from Incucyte and Other High-Throughput Platforms

boxplot_label_outliers | Standard boxplot with labeled outliers |

chou_synergy | Calculate statistics needed for Chou Synergy Curve fitting is... |

chou_synergy_CI_median | Plot single-value Chou Combination Index at IC50 |

combine_data_and_map | Combine raw data and plate map to produce a single tall data... |

convert_to_foldchange | Convert values in M1, M2 to fold-change M1 vs M2 |

create_dataset | Create a dataset from raw data without a plate map |

create_empty_plate | Create a plate list with empty elements |

create_empty_plate_map | Create an empty plate map |

create_synergy_dataset | Create a synergy dataset from raw data without a plate map |

fit_DRC | Attempt to fit a dose-response curve from the dataset and... |

fit_statistics | Fit all observations and return summary information from... |

fit_statistics_matrixes | Convert fit statistics data frame to matrixes for further... |

get_concentrations | Sorted unique list of treatment concentrations |

get_hours | Sorted unique list of hours since time zero |

get_sample_types | Sorted unique list of sample types |

get_treatments | Sorted unique list of treatments |

metric_to_grid | reshape a set of values to a matrix with axes defined by X... |

plot_chou_synergy_Fa_CI | plot FA vs. CI Chou synergy plot |

plot_color_grid | Plot a grid of colors given a matrix of numbers |

plot_fit_statistic | Plot a dose response curve summary values across one or more... |

plot.HT_fit | Plot a dose response curve from a HTfit object |

plot_synergy_interaction_index | Plot interaction index with confidence intervals for observed... |

plot_synergy_median_effect | plot FA vs. CI Chou synergy median effect plot |

plot_timecourse_raw | Plot an time course of the raw intensities |

plot_values_by_plate | Plot an image of the raw intensities for a plate |

read_dataset | Read a dataset from a text file |

read_platemap_from_excel | Read plate maps into a list of three data frames |

read_platemap_from_Incucyte_XML | Read plate maps from Incucyte plate map XML extract |

read_plates_from_Incucyte_export | Read Incucyte-formatted Excel document for a plate at one or... |

standardize_treatment_assigments | Make two treatments consistently assigned to either treatment... |

summary.HT_fit | Summarize the results of a dose response fit |

synergy_bliss | Construct synergy matrix of values expected from Bliss... |

synergy_interaction_CI | Construct confidence intervals for observed effects at... |

timecourse_AUC_ratio | Calculate AUC for sample/treatment at a concentration across... |

timecourse_relative_grid | Calculate fold-change in Dose Response Curve AUC and EC50 at... |

write_platemap_to_XML | Write a loaded plate map object in XML format |

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