Robust and User-Friendly Analysis of Growth and Fluorescence Curves

[Up] [Top]

Documentation for package ‘QurvE’ version 1.1.1

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