scMultiSim

scMultiSim simulates paired single cell RNA-seq, single cell ATAC-seq and RNA velocity data while incorporating mechanisms of gene regulatory networks, chromatin accessibility and cell-cell interactions to enable benchmarking of computational methods and assist in experimental design.

Key Features:

• Multi-modal data simulation: Generates paired single cell RNA-seq, single cell ATAC-seq and RNA velocity data simultaneously.
• Biological mechanism integration: Incorporates gene regulatory networks, chromatin accessibility and cell-cell interactions into the simulation framework.
• Parameter tuning: Allows users to control the amount of each biological factor, variation of gene-expression levels, and the influence of chromatin accessibility on RNA sequence data.

Scientific Applications:

• Method benchmarking: Evaluates and compares computational methods for single cell multi-omics data analysis.
• Experimental design: Assists in planning wet-lab experiments by simulating expected data characteristics.

Methodology:

The sources do not explicitly detail the computational steps or algorithms used in the simulation framework.