GenEx 6 free

GenEx offers advanced methods to analyze real-time qPCR data with simple mouse clicks

GenEx is a popular software for qPCR data processing and analysis.
Built in a modular fashion GenEx provides a multitude of functionalities for the qPCR community, ranging from basic real-time PCR data editing and management to advanced cutting-edge data analysis.

Basic data editing and management
Arguably the most important part of qPCR experiments is to pre-process the raw data into shape for subsequent statistical analyses. The pre-processing steps need to be performed consistently in correct order and with confidence. GenEx standard’s streamlined and user-friendly interface ensures mistake-free data handling. Intuitive and powerful presentation tools allow professional illustrations of even the most complex experimental designs.

Advanced cutting-edge data analysis
When you need more advanced analyses GenEx 7.0 is the product for you. Powerful enough to demonstrate feasibility it often proves sufficient for most users demands. Current features include parametric and non-parametric statistical tests, Hierarchical Cluster Analysis (HCA), Heatmap, Principal Component Analysis PCA), and Artificial Neural Networks. New features are continuously added to GenEx with close attention to customers’ needs.

New features
Sample handling and samples individual biology often contribute to confounding experimental variability. By using the new nested ANOVA feature in GenEx a user will be able to evaluate variance contributions from each step in the experimental procedure. With a good knowledge of the variance contributions, an appropriate distribution of experimental replicates can be selected to minimize confounding variance and maximize the power of the experimental design! For experiments with complex features, such as for example multifactorial diseases, analytical relationships and classifications may not readily be available. The support vector machine feature in the new version of GenEx is so easy to use that it will make this advanced supervised classification method easily available to novice users, while providing access to advanced parameters for experts.

Please see our Online Tutorials

TATAA and MultiD launch GenEx 7.0 – the software compliant with MIQE and CLSI guidelines
launched May 2019

TATAA Biocenter, Europe´s leading provider of genomic services using quantitative real-time PCR (qPCR), and MultiD Analyses, Europe’s prime software developer for the analysis of multivariate data, release GenEx version 6 for accurate analysis of qPCR data compliant with current MIQE guidelines and Clinical Laboratory Standards Institute (CLSI) guidelines (description below).

The new analyses in GenEx 7.0 include:   Estimating PCR efficiency, testing for outliers, testing linear model, estimating dynamic range, estimating random error, estimating limit of detection, estimating limit of quantification, estimating concentrations of unknowns, evaluation of precision, and verification of precision. For all estimates confidence intervals are calculated.   ... and much more ... download 14 days free trial version!

Additional new features include: transcript distribution for single cell analysis, Survival Analysis, Receiver Operator Characteristics (ROC), Wizard for ProSeek protein analysis, and reader for 3DGene microRNA analysis.

“I have been using GenEx for all my qPCR analyses for the past 5 years. With GenEx I can be sure that my data normalization and analyses will be MIQE compliant. Whether I’m analyzing qPCR arrays, data with a standard curve or determining a relative difference, it takes little time to import the files I need and obtain my final data set”
says Greg Shipley, President of Shipley Consulting, LLC.

“We have been using GenEx for many years at Technical University of Munich. With every new released version we are impressed by the many clever functionalities introduced for RT-qPCR analysis, especially the data normalisation and visualisation tools like PCA or HCA”,
“The new CLSI compliant analyses are most interesting to us and a natural extension of the MIQE guidelines”
says Michael W. Pfaffl.

Join all GenEx talks held at our qPCR Events -

Download the latest GenEx 7.0 trial versions -- 14 days free runtime
compare the versions:   Standard  vs.  Professional  vs.   Enterprise

GenEx Standard version
GenEx Professional version
GenEx Enterprise version
GenEx Standard GenEx
                                              Professional GenEx Enterprise
Download free trial GenEx Standard version
download free trial GenEx Professional version
download free trial GenEx Enterprise version

Purchasing GenEx 7.0 -- price list and supported instruments

GenEx can be purchased directly from bioMCC (woldwide authorized MultiD representative)  =>

Most instruments are able to export qPCR data as text export files (*.txt). GenEx is designed to easily import qPCR data from these export files in order to remove the need of manually rearranging data in Excel.

List of supported qPCR instruments by GenEx™

  • Thermo Fisher/ABI EDS files
  • QuantStudio 12K Flex (384 and 96 Wells)
  • QuantStudio OpenArray (ExpressionSuite)
  • ViiA7 (384 and 96 Wells)
  • ABI 7900 (384 and 96 Wells)
  • ABI 7500 (96 Wells)
  • ABI 7300 (96 Wells)
  • ABI StepOne
  • ABI RQ Manager for SDS 2.3 or SDS 2.4  (384 and 96 Wells)
  • BioRad CFX Manager V2 and V3 (384 and 96 Wells)
  • Roche LC480 (384 and 96 Wells)
  • Roche LC96
  • Illumina ECO
  • Biomark (Fluidigm 96 X 96  48 X 48  192 X 24) HeatMap
  • Biomark (Fluidigm 96 X 96  48 X 48  192 X 24) Table
  • Agilent MX3000/3005
  • Agilent AriaMX
  • 3D-Gene (TORAY miRNA Chips)
  • AnalytikJena
  • AnalytikJena Export Tool
  • Rotorgene
  • Thermo PikoReal
  • Douglas Scientific IntelliQube
  • WaferGene export files

GenEx 7.0 -- Release notes

  • Estimating PCR efficiency from standard curve, including confidence interval
  • Testing for outliers in a qPCR standard curve
  • Testing for linear model in a qPCR standard curve
  • Testing for dynamic range in a qPCR standard curve
  • Estimating random error of a qPCR standard curve
  • Estimating limit of detection including confidence interval of a qPCR assay/test
  • Estimating limit of quantification of a qPCR assay/test
  • Estimating concentrations including confidence intervals of unknowns based on qPCR standard curve
  • Evaluation of Precision of a qPCR assay/test
  • Verification of precision of a qPCR assay/test
Other New Analysis Features include:
  • Histogram plot for single cell analysis
  • Repeated Measures ANOVA
  • Survival Analysis
  • Receiver Operator Characteristics (ROC)
  • Wizard for ProSeek protein analysis by means of PEA (Olink)
News in GenEx update 7.0
  • In Import Wizard
    - Reader for Fluidigm Biomark Table format.
    - Reader for Thermo Fisher /ABI EDS files
    - Reader for Douglas Scientific InteliQube
    - Reader for BioRad CFX manager V3
    - Option for removing or keeping "999" values in Biomark reader
  • In Data Editor
    - Adding function "Show frequency of missing data groupwise"
    - Adding Submenu "Sort by classification column"
    - Warning generates if correction for Valid Prime is larger than 1 cycle
  • In DataManager
    - Adding ability to create classification columns based on the defined groups

... and much more!

  • GenEx Licensing
    Time limited licenses are available for 6, 12 and 24 months. Updates for the license version are for free.
  • Desktop license: License locked to one computer.
    Network concurrent Licensing: Minimum of 5 licenses setup in a network allowing GenEx to be activated on any computer with access to the network. Only available with perpetual license.
  • System Requirements
    Any modern computer running Microsoft Windows XP or later, 4 GB of RAM (8 GB or more recommended), 80 MB of available hard-disk space, display with resolution 1024 by 768 pixels or higher and scale 96 DPI. Mac users will need "Parallel" or "VM-Ware" virtual environment to run Windows.

... just download your 14 days trial version!


Volcano plot

limit of detection (LOD)

Limit of quantification (LOQ)

dynamic PCA


GenEx comes in three different packages to fulfill different customer needs:

GenEx Standard makes pre-processing of data easy!  There are options to calibrate samples with interpolate calibrators, a number of ways of handling missing data, and you can correct for primer-dimers and PCR efficiencies. Samples can also be normalized against reference genes or reference samples, the sample amounts, or a spike. If technical replicates have been made, they are easily normalized as well.

GenEx Standard is often sufficient when only one gene is studied at a time. It can be used within for example biochemistry or infection diagnostics. The package includes even more, as can be seen in the analysis list.

The data editor in GenEx lets you arrange, sort and pre-process the data.
Immunoglobulin light chain λ plotted against κ, where green represents healthy individuals and red lymphoma positive individuals.

There are statistical analyses to determine differences between two or more groups. This includes Student's t-test for paired and unpaired studies, corresponding non-parametric test, and an ANOVA test for one factor. You can also cluster your genes or samples in a dendrogram to see for example which samples show similar expression profiles. There are several options of letting you visualize the data in a plot including scatter plots, line plots, a bar plot, as well as a box and whiskers plot. The plots can be used to efficiently compare expression profiles of different samples or genes.

A 3D line plot showing how the target genes' expressions in yeast changes over time after glucose has be added to the growth medium.

GenEx Professional includes all analyses in the Standard package and much more. There are advanced multidimensional analyses such as principal component analysis (PCA) and self-organized maps (SOM) that lets you use the expression of several genes to cluster or classify samples. There are also more advanced statistical tests to determine difference of means, such as two-way ANOVA which is used when the effect that two separate factors has on the gene expression. It can be used to investigate if for instance the studied treatments influence the gene expression in a set of age groups differently.
This package is recommended when you are analyzing more than one gene in for example an exploratory study. This is often done within the medical field of research. Information of all analysis is included in the analysis list.
The package also includes several calibration analyses, such as a standard curve, reverse calibration to calibrate unknown samples to a standard curve, and a function to determine the limit of detection (LOD) for your assay.

The same data shown in the 3D line plot above is here classified in a SOM. Genes associated with glycogenesis are shown in red, glycolysis genes in blue and reference genes in green.
A standard curve has been fitted to measured data (blue line) and is shown with a confidence interval (red lines). The red dots represent unknown samples.

Our most advanced package is the GenEx Enterprise that includes all of the available analyses. The powerful multidimensional methods artificial neural networks (ANN) and support vector machines (SVM) let you build a model of your data that can be used to classify unknown samples in for example diagnostics. The models are easily shared with other GenEx users. P-curve is a form of principal component analysis (PCA) that also lets you classify unknown samples.

GenEx is excellent tool for predictive studies, when the end product is a model that can classify or calibrate unknown samples. Typical applications include diagnostics of complex diseases, and typical users are pharmaceutical companies. See the anlysis for complete overview of the included analyses.

Two genes have been used to classify unknown samples with SVM, where red indicates breast cancer and green indicates no breast cancer.
Several genes have been used to classify samples from breast cancer patients and healthy patients with p-curves.

One of the new features in GenEx is the experimental plan optimization. It can take data from a previous trial with replicates on each level (subject, sample, RT, qPCR), estimate the noise that is added at each level, and suggest an optimal experimental plan for future trials with minimum total variance under the given budget.

The optimum number of replicates at each level is presented together with the estimated total variance and total cost.

TUTORIALS Expression Profiling

Clinical Laboratory Standards Institute (CLSI)

The EP5 module in Genex implements the statistical analyses required by the guidelines in the CLSI document EP05-A2 Evaluation of Precision Performance ofQuantitative Measurement Methods; Approved Guidelines - Second Edition.
The purpose of EP05 is to evaluate the precision of clinical laboratory measurementmethods. The EP05 guidelines are intended both for developers of such methods and for users of methods who want to verify the validity of given precision claims, or just measure their own precision.
CLSI document EP05-A3  --   Evaluation of Precision Performance ofQuantitative Measurement Methods;  Approved Guidelines (3rd Edition)
The EP15 module in Genex implements the statistical analyses required by the guideline in the CLSI document EP15-A2 User Verification of Performance for Precision and Trueness; Approved Guideline - Second Edition.
The purpose of EP15 is to verify the performance of a method whose performance has previously been established by more extensive protocols. EP15 verifies the within-runprecision (the repeatability) and the within-laboratory precision. EP15 also verifies thetrueness of the method, by estimating its bias from a reference value or reference method. We give below some of the main features of the EP15 guideline, for a detailed description see the EP15-A2 document.
CLSI document EP15-A3  -- User Verification of Performance for Precision and Trueness;  Approved Guideline (3rd Edition)

MultiD Analyses AB was the first company with focus on multidimensional data analyses. It was founded in 2001 by leading scientists and software engineers from Swedish top universities who discovered that 3-dimensional data may under certain circumstances be decomposed into contributions from component specific contributions without making non-trivial assumptions. This opens totally new possibilities to analyze test samples and study chemical equilibrium, and it was considered one of the most important discoveries in analytical chemistry during the 1990-ies.

Our goal is to develop and sell software for analyses of multidimensional data. Our world unique product, DATAN, based on proprietary technology, is the most advanced software to analyze spectroscopic data. Our second unique product, GenEx, is the most advanced software available to analyze real-time PCR gene expression data.

Our main competences are in the areas of spectroscopy, fluorescence detection, data and numerical analysis, chemometry, computing, software engineering, and real-time PCR.

Purchasing GenEx 7.0 -- price list and supported instruments

GenEx can be purchased directly from bioMCC (woldwide authorized MultiD representative)  =>