TedSim: temporal d​ynamics sim​ulation of single cell RNA-sequencing data and cell division history release_c4fxwzvoxnayzddjkppvbn5xg4

Abstract

Recently, the combined scRNA-seq and CRISPR/Cas9 genome editing technologies have enabled simultaneous readouts of gene expressions and lineage barcodes, which allows for the reconstruction of the cell division tree, and makes it possible to trace the origin of each cell type. Computational methods are emerging to take advantage of the jointly profiled scRNA-seq and lineage barcode data to better reconstruct the cell division history or to infer the cell state trajectories. Here, we present TedSim (single cell Temporal dynamics Simulator), a simulator that simulates the cell division events from the root cell to present-day cells, simultaneously generating the CRISPR/Cas9 genome editing lineage barcodes and scRNA-seq data. In particular, TedSim generates cells from multiple cell types through cell division events. TedSim can be used to benchmark and investigate computational methods which use either or both of the two types of data, scRNA-seq and lineage barcodes, to study cell lineages or trajectories. TedSim is available at: https://github.com/Galaxeee/TedSim.
In application/xml+jats format

Archived Files and Locations