TSCAN

TSCAN performs pseudo-temporal ordering of cells from single-cell RNA sequencing (scRNA-seq) data via an R package implementation to reconstruct transcriptomic transitions.

Key Features:

• Pseudo-Temporal Path Construction: Constructs a pseudo-temporal path using a cluster-based minimum spanning tree (MST) built from cluster centers.
• Clustering: Reduces data complexity by clustering cells and representing clusters by their centers for subsequent graph construction.
• Cell Projection and Pseudo-time Assignment: Projects individual cells onto the MST to determine pseudo-time along the reconstructed trajectory.
• User-Driven Adjustment: Allows adjustment of cell ordering based on prior biological knowledge or experimental insights.
• Quantitative Evaluation Measures: Implements measures to objectively evaluate and compare pseudo-temporal reconstruction methods.

Scientific Applications:

• Developmental Processes: Reconstructs temporal progression of cellular states during development from scRNA-seq data.
• Differentiation Pathways: Orders cells along trajectories to identify and analyze lineage differentiation events.
• Disease Progression: Infers transcriptomic transitions relevant to disease onset and progression at the single-cell level.
• Gene Expression Dynamics: Analyzes dynamic changes in gene expression across pseudo-time in genomics and transcriptomics studies.

Methodology:

Clustering of cells to obtain cluster centers, construction of a cluster-based minimum spanning tree (MST), projection of individual cells onto the MST to assign pseudo-time, optional adjustment of ordering using prior biological knowledge, and quantitative measures to evaluate and compare pseudo-temporal reconstructions.