README.md

In Guilz/rfret: Analyze FRET Binding Data

No longer maintained

I no longer have time to maintain this package. I won't add new functionality, I won't fix bugs, I won't review or merge contributions. Use at your own risk, fork if you want.

Making this package taught me a lot. Most importantly, I realized that I tried to make it too broad in scope. A more generic non-linear curve-fitting package would still be a useful addition to the R package ecosystem (at the time of this writing), but it ought to be a lot narrower in scope and hence a lot simpler in design.

rfret: Analyze FRET Binding Data with R

This R package allows you to analyze FRET binding data and produce this kind of binding curve figure:

Given raw fluorescence data from a FRET binding experiment, you can:

1. plot all channels (donor, acceptor, FRET) to visually inspect raw data and find possible outliers;
2. average fluorescence values of technical replicates of a same experiment;
3. correct FRET signal by subtracting signal from a blank experiment;
4. guess initial values for the parameters of the binding model equation (kd, signal_min, signal_max);
5. fit a binding model equation to the data;
6. report the value of Kd;
7. plot the corrected FRET signal and the binding curve obtained by fitting the data.

This package allows batch processing and analysis of any number of datasets at a time. It can also process and analyze fluorescence polarization or anisotropy binding data. Support for fluorescence quenching data is also planned.

Installation

First, install the devtools package, if not already present on your system:

install.packages("devtools")

You can then install rfret from GitHub, right from within R:

devtools::install_github("Guilz/rfret", build_vignettes = TRUE)

Usage

You can access a detailed tutorial using the following commands:

library(rfret)
vignette("analyzing_fret_data")

Guilz/rfret documentation built on Oct. 18, 2021, 2:14 p.m.