MOSim: bulk and single-cell multi-layer regulatory network simulator

As multi-omics sequencing technologies continue to advance, the need for simulation tools that can generate realistic and diverse bulk and single-cell multi-omics datasets becomes increasingly important. We present MOSim, an R package which enables the simulation of both bulk and single-cell multi-omics data. MOSim allows for the generation of bulk transcriptomics data (RNA-seq), the incorporation of additional regulatory omics layers (ATAC-seq, miRNA-seq, ChIP-seq, Methyl-seq and Transcription Factors) and the simulation of single-cell transcriptomics data (scRNA-seq) with scATAC-seq as a regulatory layer. The tool supports various designs, including simulation of co-expression patterns of genes, simulation of replicates and differential expression between experimental conditions. MOSim provides users with the ability to generate count matrices for each simulated omics data type, capturing the heterogeneity and complexity of bulk and single-cell multi-omics datasets. Moreover, MOSim identifies differentially expressed features within each omics layer and elucidates the active regulatory relationships between regulatory omics and gene expression data at the single-cell level. By harnessing the capabilities of MOSim, researchers will be able to generate realistic and customizable bulk and single-cell multi-omics datasets, allowing them to benchmark and validate analytical methods specifically tailored for integrative analysis of diverse regulatory omics data. ### Competing Interest Statement The authors have declared no competing interest.