Algorithms
CellNet: CellNet is a network-biology-based, computational platform that assesses the fidelity of cellular engineering and generates hypotheses for improving cell derivations. CellNet is based on the reconstruction of cell type-specific gene regulatory networks (GRNs), which we performed using publicly available RNA-Seq data of 16 mouse and 16 human cell and tissue types.
CellRouter: CellRouter is a multifaceted single-cell analysis platform that identifies complex cell-state transition trajectories by exploring the subpopulation structure of multi-dimensional, single-cell omics data. CellRouter integrates subpopulation identification, single-cell trajectories, and gene regulatory networks (GRNs) to provide new insights into cell-state transitions during lineage diversification, convergence, or cell reprogramming.
CellCommunicator: CellCommunicator is an algorithm to reconstruct intercellular communication networks and signalling pathways activated upon cell-cell interactions from single-cell RNA sequencing data.