MERLoT

MERLoT reconstructs lineage tree topologies and imputes temporal gene expression profiles from single-cell RNA sequencing (scRNA-seq) data to elucidate cellular differentiation and heterogeneity.

Key Features:

• Complex Lineage Tree Reconstruction: Reconstructs detailed lineage tree topologies that capture multiple cell fates from scRNA-seq-derived data.
• Temporal Gene Expression Imputation: Imputes temporal gene expression profiles along reconstructed lineage branches to reveal dynamic transcriptional changes during differentiation.
• R package implementation: Implemented as an R package for analysis of scRNA-seq data.
• Benchmarking and Simulation Support: Provides benchmarking and plotting scripts and supplies example expression matrices and parameter files via the GWDG FTP server for simulations and validation.

Scientific Applications:

• Cellular differentiation and heterogeneity analysis: Reconstruction of differentiation pathways and temporal emergence of cell types from scRNA-seq datasets.
• Method benchmarking and validation: Validation and comparison of lineage reconstruction approaches using both real-case and simulated scRNA-seq datasets.

Methodology:

Uses coordinates for cells within a given manifold (such as diffusion maps) as input data to reconstruct lineage tree topologies.