bio-single-cell-lineage-tracing
Reconstruct cell lineage trees from CRISPR barcode tracing or mitochondrial mutations. Use when studying clonal dynamics, cell fate decisions, or developmental trajectories.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-lineage-tracing --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: Cassiopeia 2.0+, matplotlib 3.8+, numpy 1.26+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Lineage Tracing Analysis **"Reconstruct cell lineage trees from CRISPR barcodes"** → Build phylogenetic trees of cell relationships from lineage barcode mutations to study clonal dynamics and cell fate decisions. - Python: `cassiopeia.tl.ILPSolver(cas_tree)` or `GreedySolver` for tree reconstruction ## Cassiopeia Tree Reconstruction **Goal:** Reconstruct a cell lineage tree from CRISPR barcode character matrices to reveal clonal relationships among single cells. **Approach:** Load a character matrix (cells x barcode sites with mutation states), create a CassiopeiaTree object, then solve with a greedy or ILP maximum parsimony solver. ```python import cassiopeia as cas import numpy as np # Load character matrix (cells x barcode sites) # Values: mutation
- Version Compatibility
- Cassiopeia Tree Reconstruction
- Hybrid Solvers
- From CRISPR Barcodes
- Character Matrix QC
- CoSpar for Clonal Dynamics
- CoSpar Trajectory Analysis
- Mitochondrial Lineage (MitoTracing)
- LARRY Barcode Processing
- Tree Visualization
- Tree Quality Metrics
- Integrate with scRNA-seq
- Clonal Expansion Analysis
- Tree Statistics
What does the bio-single-cell-lineage-tracing skill do?
Reconstruct cell lineage trees from CRISPR barcode tracing or mitochondrial mutations. Use when studying clonal dynamics, cell fate decisions, or developmental trajectories.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-lineage-tracing --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.