bio-single-cell-lineage-tracing

What problem does it solve?

Reconstruct lineage trees and track clonal dynamics from CRISPR barcode data and mitochondrial mutations in single-cell experiments, enabling researchers to infer developmental trajectories from high-dimensional measurements.

Core Features & Use Cases

• Cassiopeia-based lineage reconstruction from barcode matrices to reveal clonal relationships.
• CoSpar-enabled analysis of clonal dynamics and fate maps using time-series data.
• MitoTracing workflows to leverage mitochondrial mutations for lineage inference alongside barcodes.
• End-to-end guidance for integrating with scRNA-seq data and metadata to annotate trees.

Quick Start

Provide barcode data (CRISPR barcodes or mtDNA variants) and run the Cassiopeia-CoSpar workflow to reconstruct a lineage tree and analyze clonal dynamics.