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QurvE (version 1.1.1)

Robust and User-Friendly Analysis of Growth and Fluorescence Curves

Description

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) .

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Version

Install

install.packages('QurvE')

Monthly Downloads

267

Version

1.1.1

License

GPL (>= 3)

Issues

1

Pull Requests

0

Stars

25

Forks

5

Maintainer

Nicolas T. Wirth

Last Published

January 26th, 2024

Functions in QurvE (1.1.1)

flFitLinear

Data fit via a heuristic linear method
growth.control

Create a grofit.control object.
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.
flFitSpline

Perform a smooth spline fit on fluorescence data
flFit

Perform a fluorescence curve analysis on all samples in the provided dataset.
growth.drFitSpline

Perform a smooth spline fit on response vs. concentration data of a single sample to determine the EC50.
growth.drBootSpline

Perform a smooth spline fit on response vs. concentration data of a single sample
flBootSpline

flBootSpline: Function to generate a bootstrap
growth.gcBootSpline

Perform a bootstrap on growth vs. time data followed by spline fits for each resample
lm_parms

Helper functions for handling linear fits.
growth.gcFitModel

Fit nonlinear growth models to growth data
growth.gcFit

Perform a growth curve analysis on all samples in the provided dataset.
inflect

Find indices of maxima an minima in a data series
parse_Gen5Gen6

Extract relevant data from a raw data export file generated with the "Gen5" or "Gen6" software.
growth.workflow

Run a complete growth curve analysis and dose-reponse analysis workflow.
growth.report

Create a PDF and HTML report with results from a growth curve analysis workflow
low.integrate

Function to estimate the area under a curve given as x and y(x) values
growth.gcFitLinear

Fit an exponential growth model with a heuristic linear method
growth.gcFitSpline

Perform a smooth spline fit on growth data
plot.drFitSpline

Generic plot function for drFitSpline objects.
parse_victornivo

Extract relevant data from a raw data export file generated from the software of Perkin Elmer's "Victor Nivo" plate readers.
parse_data

Parse raw plate reader data and convert it to a format compatible with QurvE
plot.drFitFLModel

Generic plot function for drFitFLModel objects.
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.drFitfl

Generic plot function for drFitFL objects.
plot.drFit

Generic plot function for drFit objects.
plot.drFitModel

Generic plot function for drFitModel objects.
plot.dr_parameter

Compare calculated dose-response parameters between conditions.
plot.dual

Compare fluorescence and growth over time
plot.gcFitLinear

Generic plot function for gcFittedLinear objects. Plot the results of a linear regression on ln-transformed data
plot.flBootSpline

Generic plot function for flBootSpline objects.
plot.gcBootSpline

Generic plot function for gcBootSpline objects.
plot.gcFitModel

Generic plot function for gcFitModel objects.
plot.gcFitSpline

Generic plot function for gcFitSpline objects.
plot.flFitRes

Combine different groups of samples into a single plot
plot.grid

Plot a matrix of growth curve panels
plot.flFitLinear

Generic plot function for flcFittedLinear objects. Plot the results of a linear regression on ln-transformed data
plot.flFitSpline

Generic plot function for flFitSpline objects.
summary.drBootSpline

Generic summary function for drBootSpline objects
summary.drFit

Generic summary function for drFit objects
plot.parameter

Compare growth parameters between samples or conditions
read_data

Read growth and fluorescence data in table format
plot.grofit

Generic plot function for grofit objects. Combine different groups of samples into a single plot
run_app

Run Shiny QurvE App
read_file

Call the appropriate function required to read a table file and return the table as a dataframe object.
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.
plot.grodata

Generic plot function for grodata objects. Plots raw growth, fluorescence, or normalized fluorescence data of multiple samples or conditions.
summary.drFitFLModel

Generic summary function for drFitFLModel objects
summary.drFitModel

Generic summary function for drFitModel objects
summary.flFitSpline

Generic summary function for flFitSpline objects
summary.flBootSpline

Generic summary function for flBootSpline objects
summary.gcFit

Generic summary function for gcFit objects
summary.gcBootSpline

Generic summary function for gcBootSpline objects
summary.flFitLinear

Generic summary function for flFitLinear objects
summary.drFitfl

Generic summary function for drFitfl objects
summary.flFit

Generic summary function for flFit objects
summary.gcFitLinear

Generic summary function for gcFitLinear objects
summary.drFitSpline

Generic summary function for drFitSpline objects
table_group_growth_spline

Generate a grouped results table for spline fits with average and standard deviations
updateResistantPopover

Create an update-resistant popover for a Shiny element
summary.gcFitModel

Generic summary function for gcFitModel objects
tidy_to_custom

Convert a tidy data frame to a custom QurvE format
summary.gcFitSpline

Generic summary function for gcFitSpline objects
zipFastener

Combine two dataframes like a zip-fastener
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_model

Generate a grouped results table for parametric fits with average and standard deviations
table_group_growth_linear

Generate a grouped results table for linear fits with average and standard deviations
buildTooltipOrPopoverOptionsList

Custom tooltip function
biosensor.eq

Internal function used to fit a biosensor response model with nlsLM
export_Table

Export a tabular object as tab-separated .txt file
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.
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.
export_RData

Export an R object as .RData file
fl.control

Create a fl.control object.
QurvE-package

QurvE: Robust and User-Friendly Analysis of Growth and Fluorescence Curves