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Mikael Kubista, Amin Forootan Amin Forootan1, Björn Sjögreen1, Mikael Kubista2 1) Multid Analyses AB, Sweden; 2) TATAA Biocenter, Sweden |
Abstract
With the emergence of RNA sequencing (RNASeq) transcriptome profiling entered a new era. High throughput high quality whole transcriptome data can today be collected routinely. The challenge is no longer acquiring data but rather analyzing and interpreting them. Analysis includes validating data quality, merging runs, normalizing the data, comparing experimental conditions, testing hypothesis and interpreting the results. GenEx is the most used software for qPCR data analysis and with the launch of GenEx 7, here at the 9th Gene Quantification Event, also RNASeq data can readily be analyzed. GenEx is developed for experimentalists, with a user-friendly intuitive interface that provides a smooth analytical workflow for statistical analyses of the data in compliance with guidelines when relevant. Very large data sets, typical of RNASeq, are easily and rapidly handled and graphical interfaces allow interactive analyses with powerful methods such as DESeq2, and Normfinder for normalization, t-test, Mann-Whitney, Wilcoxon’s test and ANOVA models for group comparisons, hierarchical clustering, self-organizing maps (SOM) and principal component analysis (PCA) for clustering, dynamic PCA with statistical filters for variable selection to find the most relevant expression markers, kinetic PCA for time studies, survival analysis to compare treatments, and artificial neural network (ANN) and support vector machines (SVM) to build predictive models. GenEx 7 is continuously updated to include new methods and strategies as they become available and to maintain compatibility with qPCR and NGS instrument software, computer operating systems, and graphical and printer routines. GenEx 7 is the only data analysis software supported by the majority of leading instrument and solution providers.
Download the latest GenEx version here.
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