The 'ExpHunterSuite' is an R package designed to analyze high-throughput gene expression data comprehensively. It encompasses various approaches, including co-expression module detection, data-fusion for result integration, threshold-based methods, and a Naïve Bayes classifier trained on simulated data. The tool is applied to rare-disease model datasets, confirming existing knowledge and suggesting novel hypotheses. Through application to simulated and spike-in experiments, the package demonstrates the effectiveness of combining multiple methods using consensus and classifiers to achieve optimal results. 'ExpHunterSuite' is versatile, applicable to both model and non-model organisms, and offers modular usage in R or command-line execution for scalability with large datasets.