MOSim: bulk and single-cell multilayer regulatory network simulator.

Area of Science:

• Computational Biology
• Bioinformatics
• Genomics

Background:

• Advancing multi-omics sequencing technologies necessitate robust simulation tools.
• Current tools often lack the ability to generate diverse, realistic multi-omics datasets for method validation.

Purpose of the Study:

• To introduce MOSim, an R package designed for simulating both bulk and single-cell multi-omics data.
• To provide a versatile tool for generating customizable datasets for benchmarking analytical methods.

Main Methods:

• MOSim simulates bulk (mosim function) and single-cell (sc_mosim function) multi-omics data.
• It integrates transcriptomics (RNA-seq, scRNA-seq) with regulatory omics layers (ATAC-seq, miRNA-seq, ChIP-seq, Methyl-seq, transcription factors).
• Supports simulation of gene co-expression, replicates, and differential expression.

Main Results:

• MOSim generates quantification matrices for various omics data types, reflecting dataset complexity.
• Identifies differentially abundant features and active regulatory relationships across omics layers.
• Enables simulation of both bulk and single-cell multi-omics data.

Conclusions:

• MOSim facilitates the generation of realistic, customizable multi-omics datasets.
• It is a valuable resource for benchmarking and validating integrative analysis methods.
• Supports researchers in analyzing complex biological systems through simulated data.