domains / families / science / lineage-tracing

lineage-tracing

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Reconstructs single-cell lineage trees and clonal relationships from CRISPR/Cas9 scars, static expressed barcodes (LARRY/CellTag), or somatic mtDNA mutations using Cassiopeia, Startle, and CoSpar. Use when building a phylogeny from barcode scars, choosing a tree-reconstruction solver, handling homoplasy and dropout, grouping clones from mtDNA, integrating clone with transcriptomic state, or judging whether a state-based fate call is trustworthy.

When to use

• building a phylogeny from barcode scars
• choosing a tree-reconstruction solver
• handling homoplasy and dropout
• grouping clones from mtDNA
• integrating clone with transcriptomic state
• judging whether a state-based fate call is trustworthy

When not to use

• purely state-based trajectory methods
• native human tissue without engineering for CRISPR scars

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