# Robust and User-Friendly Analysis of Growth and Fluorescence Curves

## Documentation for package ‘QurvE’ version 1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

biosensor.eq | Internal function used to fit a biosensor response model with 'nlsLM'
export_RData | Export an R object as .RData file
export_Table | Export a tabular object as tab-separated .txt file
fl.control | Create a 'fl.control' object.
fl.drFit | Fit a biosensor model (Meyer et al., 2019) to response vs. concentration data
fl.drFitModel | Perform a biosensor model fit on response vs. concentration data of a single sample.
fl.report | Create a PDF and HTML report with results from a fluorescence analysis workflow
fl.workflow | Run a complete fluorescence curve analysis and dose-reponse analysis workflow.
flBootSpline | flBootSpline: Function to generate a bootstrap
flFit | Perform a fluorescence curve analysis on all samples in the provided dataset.
flFitLinear | Data fit via a heuristic linear method
flFitSpline | Perform a smooth spline fit on fluorescence data
growth.control | Create a 'grofit.control' object.
growth.drBootSpline | Perform a smooth spline fit on response vs. concentration data of a single sample
growth.drFit | Perform a dose-response analysis on response vs. concentration data
growth.drFitModel | Fit various models to response vs. concentration data of a single sample to determine the EC50.
growth.drFitSpline | Perform a smooth spline fit on response vs. concentration data of a single sample to determine the EC50.
growth.gcBootSpline | Perform a bootstrap on growth vs. time data followed by spline fits for each resample
growth.gcFit | Perform a growth curve analysis on all samples in the provided dataset.
growth.gcFitLinear | Fit an exponential growth model with a heuristic linear method
growth.gcFitModel | Fit nonlinear growth models to growth data
growth.gcFitSpline | Perform a smooth spline fit on growth data
growth.report | Create a PDF and HTML report with results from a growth curve analysis workflow
growth.workflow | Run a complete growth curve analysis and dose-reponse analysis workflow.
inflect | Find indices of maxima an minima in a data series
lm_parms | Helper functions for handling linear fits.
lm_window | Helper functions for handling linear fits.
low.integrate | Function to estimate the area under a curve given as x and y(x) values
parse_data | Parse raw plate reader data and convert it to a format compatible with QurvE
parse_Gen5Gen6 | Extract relevant data from a raw data export file generated with the "Gen5" or "Gen6" software.
parse_victornivo | Extract relevant data from a raw data export file generated from the software of Perkin Elmer's "Victor Nivo" plate readers.
parse_victorx3 | Extract relevant data from a raw data export file generated from the software of Perkin Elmer's "Victor X3" plate readers.
plot.drBootSpline | Generic plot function for 'gcBootSpline' objects.
plot.drFit | Generic plot function for 'drFit' objects.
plot.drFitfl | Generic plot function for 'drFitFL' objects.
plot.drFitFLModel | Generic plot function for 'drFitFLModel' objects.
plot.drFitModel | Generic plot function for 'drFitModel' objects.
plot.drFitSpline | Generic plot function for 'drFitSpline' objects.
plot.dr_parameter | Compare calculated dose-response parameters between conditions.
plot.dual | Compare fluorescence and growth over time
plot.flBootSpline | Generic plot function for 'flBootSpline' objects.
plot.flFit | Combine different groups of samples into a single plot
plot.flFitLinear | Generic plot function for 'flcFittedLinear' objects. Plot the results of a linear regression on ln-transformed data
plot.flFitRes | Combine different groups of samples into a single plot
plot.flFitSpline | Generic plot function for 'flFitSpline' objects.
plot.gcBootSpline | Generic plot function for 'gcBootSpline' objects.
plot.gcFitLinear | Generic plot function for 'gcFittedLinear' objects. Plot the results of a linear regression on ln-transformed data
plot.gcFitModel | Generic plot function for 'gcFitModel' objects.
plot.gcFitSpline | Generic plot function for 'gcFitSpline' objects.
plot.grid | Plot a matrix of growth curve panels
plot.grodata | Generic plot function for 'grodata' objects. Plots raw growth, fluorescence, or normalized fluorescence data of multiple samples or conditions.
plot.grofit | Generic plot function for 'grofit' objects. Combine different groups of samples into a single plot
plot.parameter | Compare growth parameters between samples or conditions
rdm.data | The function calls the 'baranyi' function to generate curves between time zero and 't' and adds some random noise to the x- and y-axes. The three growth parameters given as input values will be slightly changed to produce different growth curves. The resulting datasets can be used to test the 'growth.workflow' function.
read_data | Read growth and fluorescence data in table format
read_file | Call the appropriate function required to read a table file and return the table as a dataframe object.
run_app | Run Shiny QurvE App
summary.drBootSpline | Generic summary function for drBootSpline objects
summary.drFit | Generic summary function for drFit objects
summary.drFitfl | Generic summary function for drFitfl objects
summary.drFitFLModel | Generic summary function for drFitFLModel objects
summary.drFitModel | Generic summary function for drFitModel objects
summary.drFitSpline | Generic summary function for drFitSpline objects
summary.flBootSpline | Generic summary function for flBootSpline objects
summary.flFit | Generic summary function for flFit objects
summary.flFitLinear | Generic summary function for flFitLinear objects
summary.flFitSpline | Generic summary function for flFitSpline objects
summary.gcBootSpline | Generic summary function for gcBootSpline objects
summary.gcFit | Generic summary function for gcFit objects
summary.gcFitLinear | Generic summary function for gcFitLinear objects
summary.gcFitModel | Generic summary function for gcFitModel objects
summary.gcFitSpline | Generic summary function for gcFitSpline objects
table_group_fluorescence_linear | Generate a grouped results table for linear fits with average and standard deviations
table_group_fluorescence_spline | Generate a grouped results table for spline fits with average and standard deviations
table_group_growth_linear | Generate a grouped results table for linear fits with average and standard deviations
table_group_growth_model | Generate a grouped results table for parametric fits with average and standard deviations
table_group_growth_spline | Generate a grouped results table for spline fits with average and standard deviations
zipFastener | Combine two dataframes like a zip-fastener