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Martin Modrák edited this page Mar 30, 2023
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Genexpi is a tool to infer or validate genetic networks based on expression time series data. Multiple interfaces are being developed.
- CyGenexpi - a Cytoscape interface
- R
- Command line
- Matlab (unfortunately currently available only on request) - this one was used in the DNA mapping and kinetic modelling of the HrdB regulon in Streptomyces coelicolor paper. The Matlab interface works via calling the Command line interface.
The core of the inference engine is written in OpenCL wrapped in Java and is contained in the genexpi-compute folder. For more details on the method see the Genexpi paper in BMC Bioinformatics