MOSim

MOSim simulates realistic multi-omic datasets including bulk RNA-seq, scRNA-seq, ATAC-seq, scATAC-seq, miRNA-seq, ChIP-seq, Methyl-seq and transcription factor regulatory layers to enable benchmarking and experimental design.

Key Features:

• Comprehensive omics coverage: Supports bulk transcriptomics (RNA-seq), single-cell transcriptomics (scRNA-seq), ATAC-seq and scATAC-seq, miRNA-seq, ChIP-seq, Methyl-seq and transcription factor regulatory layers.
• Simulation of complex regulatory relationships: Simulates intricate many-to-many regulatory interactions across molecular layers capturing heterogeneity and regulatory complexity.
• Flexible experimental design: Simulates gene co-expression patterns, generates biological replicates, and models differential expression between conditions.
• Customization and parameterization: Allows adjustment of simulation parameters to create count matrices and multilayer regulatory networks reflecting diverse omics types.
• Quantification matrices and differential features: Generates quantification matrices per omics type and reports differentially abundant features and active regulatory relationships between regulatory omics and gene expression at bulk and single-cell levels.

Scientific Applications:

• Method testing and benchmarking: Generates customizable multi-omic datasets for testing and benchmarking integrative analysis methods.
• Experimental design validation: Simulates expected outcomes under varied conditions to validate and compare experimental designs.

Methodology:

Implemented as an R package; generates count matrices and multilayer regulatory networks by simulating gene co-expression, biological replicates, differential expression, and many-to-many regulatory interactions for bulk and single-cell omics, and outputs quantification matrices and lists of differentially abundant features.