TedSim

TedSim simulates cell division trajectories and generates paired CRISPR/Cas9 lineage barcodes and single-cell RNA-seq (scRNA-seq) profiles to model cellular lineage dynamics.

Key Features:

• Simultaneous Data Generation: Generates CRISPR/Cas9 genome-editing lineage barcodes and scRNA-seq expression profiles from the same simulated cells.
• Cell Division Simulation: Simulates cell division events starting from an ancestral root cell and models proliferation and differentiation into multiple cell types over time.
• Benchmarking Computational Methods: Produces simulated datasets for evaluating algorithms that reconstruct cell division histories, infer cellular state trajectories, and analyze lineage barcodes with scRNA-seq data.

Scientific Applications:

• Cell lineage reconstruction: Reconstruct lineage trees and trace ancestry of cells using paired barcode and expression data.
• Ancestral cell identification: Identify ancestral or root cell states within simulated lineages.
• Trajectory inference: Test and validate trajectory inference methods using combined lineage barcode and scRNA-seq simulations.
• Developmental biology: Model developmental processes and differentiation dynamics.
• Cancer progression: Study tumor evolution and clonal dynamics through simulated lineage and expression data.
• Regenerative medicine: Investigate lineage relationships relevant to tissue regeneration and repair.

Methodology:

Generates simulated scRNA-seq profiles together with CRISPR/Cas9-derived lineage barcodes from a simulated cell division process to produce paired datasets for lineage reconstruction and trajectory analysis.