Robust and User-Friendly Analysis of Growth and Fluorescence Curves
A palette with 40 colors
Internal function used to fit a biosensor response model with nlsLM
Custom tooltip function
Export an R object as .RData file
Export a tabular object as tab-separated .txt file
Create a fl.control object.
Fit a biosensor model (Meyer et al., 2019) to response vs. concentrati...
Perform a biosensor model fit on response vs. concentration data of a ...
Create a PDF and HTML report with results from a fluorescence analysis...
Run a complete fluorescence curve analysis and dose-reponse analysis w...
flBootSpline: Function to generate a bootstrap
Perform a fluorescence curve analysis on all samples in the provided d...
Data fit via a heuristic linear method
Perform a smooth spline fit on fluorescence data
Create a grofit.control object.
Perform a smooth spline fit on response vs. concentration data of a si...
Perform a dose-response analysis on response vs. concentration data
Fit various models to response vs. concentration data of a single samp...
Perform a smooth spline fit on response vs. concentration data of a si...
Perform a bootstrap on growth vs. time data followed by spline fits fo...
Perform a growth curve analysis on all samples in the provided dataset...
Fit an exponential growth model with a heuristic linear method
Fit nonlinear growth models to growth data
Perform a smooth spline fit on growth data
Create a PDF and HTML report with results from a growth curve analysis...
Run a complete growth curve analysis and dose-reponse analysis workflo...
Find indices of maxima an minima in a data series
Helper functions for handling linear fits.
Function to estimate the area under a curve given as x and y(x) values
Parse raw plate reader data and convert it to a format compatible with...
Extract relevant data from a raw data export file generated with the "...
Extract relevant data from a raw data export file generated from the s...
Extract relevant data from a raw data export file generated from the s...
Compare calculated dose-response parameters between conditions.
Generic plot function for gcBootSpline objects.
Generic plot function for drFit objects.
Generic plot function for drFitFL objects.
Generic plot function for drFitFLModel objects.
Generic plot function for drFitModel objects.
Generic plot function for drFitSpline objects.
Compare fluorescence and growth over time
Generic plot function for flBootSpline objects.
Generic plot function for flcFittedLinear objects. Plot the results ...
Combine different groups of samples into a single plot
Generic plot function for flFitSpline objects.
Generic plot function for gcBootSpline objects.
Generic plot function for gcFittedLinear objects. Plot the results o...
Generic plot function for gcFitModel objects.
Generic plot function for gcFitSpline objects.
Plot a matrix of growth curve panels
Generic plot function for grodata objects. Plots raw growth, fluores...
Generic plot function for grofit objects. Combine different groups o...
Compare growth parameters between samples or conditions
QurvE: Robust and User-Friendly Analysis of Growth and Fluorescence Cu...
The function calls the baranyi function to generate curves between t...
Read growth and fluorescence data in table format
Call the appropriate function required to read a table file and return...
Run Shiny QurvE App
Single hue palettes for ggplot2
Generic summary function for drBootSpline objects
Generic summary function for drFit objects
Generic summary function for drFitfl objects
Generic summary function for drFitFLModel objects
Generic summary function for drFitModel objects
Generic summary function for drFitSpline objects
Generic summary function for flBootSpline objects
Generic summary function for flFit objects
Generic summary function for flFitLinear objects
Generic summary function for flFitSpline objects
Generic summary function for gcBootSpline objects
Generic summary function for gcFit objects
Generic summary function for gcFitLinear objects
Generic summary function for gcFitModel objects
Generic summary function for gcFitSpline objects
Generate a grouped results table for linear fits with average and stan...
Generate a grouped results table for spline fits with average and stan...
Generate a grouped results table for linear fits with average and stan...
Generate a grouped results table for parametric fits with average and ...
Generate a grouped results table for spline fits with average and stan...
Convert a tidy data frame to a custom QurvE format
Create an update-resistant popover for a Shiny element
Combine two dataframes like a zip-fastener
High-throughput analysis of growth curves and fluorescence data using three methods: linear regression, growth model fitting, and smooth spline fit. Analysis of dose-response relationships via smoothing splines or dose-response models. Complete data analysis workflows can be executed in a single step via user-friendly wrapper functions. The results of these workflows are summarized in detailed reports as well as intuitively navigable 'R' data containers. A 'shiny' application provides access to all features without requiring any programming knowledge. The package is described in further detail in Wirth et al. (2023) <doi:10.1038/s41596-023-00850-7>.
Useful links