Universität Innsbruck

qRATqPCR relative expression analysis tool

qRAT is a R based standalone desktop application designed to provide a comprehensive, simple and easy to use tool for the relative quantification of real-time quantitative PCR data analysis. Functions are provided for users who have little statistical and no R programming background.


Web application

qRAT is available as web application on ShinyApps.io:

Latest Release: 0.2.0

Linux and MacOS

Linux and MacOS users can run the app using R console and RStudio. Please follow the instructions on GitHub.


qRAT standalone is currently not available as easy-install for Windows.


If you use qRAT for any published research, please include the following citation:

Flatschacher, D., Speckbacher, V. & Zeilinger, S. qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data. BMC Bioinformatics 23, 286 (2022). https://doi.org/10.1186/s12859-022-04823-7

What's qRAT?

qRAT is a R based standalone desktop application to automate the processing of raw Quantification Cycle (Cq) data files exported from virtually any qPCR instrument using well established and state-of-the-art statistical and graphical techniques. The purpose of this tool is to provide a comprehensive, straightforward, and easy-to-use solution for the relative quantification of RT-qPCR data that requires no programming knowledge or additional software installation.

The current implementation allows ΔCq calculation (relative to endogenous control(s)), ΔΔCq calculation (relative to endogenous control(s) and a reference sample) and inter-plate variation correction. Moreover, functionalities for parsing, filtering and visualisation of relative RT-qPCR data are included.

Getting Help

The User Guide gives a extensive documentation on data input, data analysis and graphical representation of the application. You can download the User Guide >right here< or access it directly from within the qRAT application.
Example datasets can be downloaded >here<

  The documentation, alongside the app, is under constant development. If you see any mistakes or typos, please let us know.

Made with

qRAT is using various applications, tools and scripts originating from external sources (open-source third party software). Within this section, all tools and packages are listed. Keep in mind that most of the packages may also depend on other packages not listed here. Please follow the web links if you want to get more information on a specific package or tool.

R Packages

  • Bslib
  • DT
  • HTqPCR
  • RInno
  • data.table
  • ddCt
  • dplyr
  • DT
  • ggplot2
  • magrittr
  • plotly
  • scales
  • shiny
  • shinycssloaders
  • shinyWidgets
  • shinyjs
  • stringr
  • tidyr
  • waiter
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