Man pages for DavidQuigley/HTDoseResponseCurve
Dose Response Curve Evaluation from Incucyte and Other High-Throughput Platforms

boxplot_label_outliersStandard boxplot with labeled outliers
chou_synergyCalculate statistics needed for Chou Synergy Curve fitting is...
chou_synergy_CI_medianPlot single-value Chou Combination Index at IC50
combine_data_and_mapCombine raw data and plate map to produce a single tall data...
convert_to_foldchangeConvert values in M1, M2 to fold-change M1 vs M2
create_datasetCreate a dataset from raw data without a plate map
create_empty_plateCreate a plate list with empty elements
create_empty_plate_mapCreate an empty plate map
create_synergy_datasetCreate a synergy dataset from raw data without a plate map
fit_DRCAttempt to fit a dose-response curve from the dataset and...
fit_statisticsFit all observations and return summary information from...
fit_statistics_matrixesConvert fit statistics data frame to matrixes for further...
get_concentrationsSorted unique list of treatment concentrations
get_hoursSorted unique list of hours since time zero
get_sample_typesSorted unique list of sample types
get_treatmentsSorted unique list of treatments
metric_to_gridreshape a set of values to a matrix with axes defined by X...
plot_chou_synergy_Fa_CIplot FA vs. CI Chou synergy plot
plot_color_gridPlot a grid of colors given a matrix of numbers
plot_fit_statisticPlot a dose response curve summary values across one or more...
plot.HT_fitPlot a dose response curve from a HTfit object
plot_synergy_interaction_indexPlot interaction index with confidence intervals for observed...
plot_synergy_median_effectplot FA vs. CI Chou synergy median effect plot
plot_timecourse_rawPlot an time course of the raw intensities
plot_values_by_platePlot an image of the raw intensities for a plate
read_datasetRead a dataset from a text file
read_platemap_from_excelRead plate maps into a list of three data frames
read_platemap_from_Incucyte_XMLRead plate maps from Incucyte plate map XML extract
read_plates_from_Incucyte_exportRead Incucyte-formatted Excel document for a plate at one or...
standardize_treatment_assigmentsMake two treatments consistently assigned to either treatment...
summary.HT_fitSummarize the results of a dose response fit
synergy_blissConstruct synergy matrix of values expected from Bliss...
synergy_interaction_CIConstruct confidence intervals for observed effects at...
timecourse_AUC_ratioCalculate AUC for sample/treatment at a concentration across...
timecourse_relative_gridCalculate fold-change in Dose Response Curve AUC and EC50 at...
write_platemap_to_XMLWrite a loaded plate map object in XML format
DavidQuigley/HTDoseResponseCurve documentation built on June 2, 2017, 5:44 a.m.