Totem

Totem infers tree-shaped trajectories from single-cell RNA sequencing (scRNA-seq) data to model cell differentiation and lineage structure.

Key Features:

• Tree-Shaped Trajectory Inference: Infers linear, bifurcating, multifurcating and other tree-shaped trajectories from scRNA-seq data.
• Integration with Slingshot: Employs the Slingshot algorithm to identify and refine linear curves within lineage trees.
• Automatic Clustering and Topology Estimation: Generates multiple clustering results and estimates their topologies as minimum spanning trees.
• Cell Connectivity Analysis: Measures connectivity between cells to identify branching points and milestones within inferred trajectories.
• Rapid Testing of Alternative Trajectories: Facilitates testing and comparison of multiple trajectory models derived from clustering results.

Scientific Applications:

• Cell differentiation pathways: Reconstruction and analysis of differentiation trajectories and branching events from scRNA-seq data.
• Developmental biology: Reconstruction of lineage trees and identification of developmental milestones and lineage specification events.
• Cancer progression and cellular dynamics: Analysis of tumor cell lineage changes and branching behaviors during cancer progression and other dynamic processes.

Methodology:

Generates multiple clustering results from scRNA-seq data, estimates cluster topologies as minimum spanning trees, measures cell connectivity, and applies Slingshot to identify and refine linear lineage curves.