SEMgraph: an R package for causal network inference of high-throughput data with structural equation models

Abstract Motivation With the advent of high-throughput sequencing in molecular biology and medicine, the need for scalable statistical solutions for modeling complex biological systems has become of critical importance. The increasing number of platforms and possible experimental scenarios raised the problem of integrating large amounts of new heterogeneous data and current knowledge, to test novel hypotheses and improve our comprehension of physiological processes and diseases. Results Combining network analysis and causal inference within the framework of structural equation modeling (SEM), we developed the R package SEMgraph. It provides a fully automated toolkit, managing complex biological systems as multivariate networks, ensuring robustness and reproducibility through data-driven evaluation of model architecture and perturbation, which is readily interpretable in terms of causal effects among system components. Availability and implementation SEMgraph package is available at https://cran.r-project.org/web/packages/SEMgraph. Supplementary information Supplementary data are available at Bioinformatics online.