CEMiTool

CEMiTool is a software tool developed for analyzing modular gene co-expression networks. This method is commonly used in the study of genes to understand their systems-level functionality, providing a basis for discovering clinically relevant molecular pathways underlying different diseases and conditions.

The CEMiTool provides a fast and easy-to-use method for discovering and analyzing co-expression modules. CEMiTool outperforms existing tools and provides unique results in a user-friendly html report with high-quality graphs. Among its features, the tool evaluates whether modules contain genes over-represented by specific pathways or altered in a specific sample group. Additionally, it integrates transcriptomic data with interactome information, identifying the potential hubs on each network.

The tool has been successfully applied to over 1000 transcriptome datasets and a new RNA-seq dataset of patients infected with Leishmania, revealing novel insights into the disease's physiopathology. The CEMiTool R package provides users with an easy-to-use method to automatically implement gene co-expression network analyses, obtain key information about the discovered gene modules using additional downstream analyses, and retrieve publication-ready results via a high-quality interactive report.