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Scanpy dpt trajectory starter

Skill ma-compbio-lab/SkillFoundry/skills/transcriptomics/scanpy-dpt-trajectory-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill scanpy-dpt-trajectory-starter

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SKILL.md

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Scanpy DPT Trajectory Starter

Use this skill to compute a deterministic toy diffusion-pseudotime trajectory with Scanpy tl.dpt.

What it does

  • Loads a tiny genes-by-cells matrix and a root cell.
  • Builds a Scanpy neighbors graph, computes diffusion components, and runs tl.dpt.
  • Exports per-cell pseudotime values and the inferred cell order.

When to use it

  • You need a verified starter for the trajectory inference leaf in transcriptomics.
  • You want a bounded example of DPT before moving to larger pseudotime workflows.
  • You need deterministic JSON output that can be checked in repository tests.

Example

slurm/envs/scanpy/bin/python skills/transcriptomics/scanpy-dpt-trajectory-starter/scripts/run_scanpy_dpt_trajectory.py \
  --counts skills/transcriptomics/scanpy-dpt-trajectory-starter/examples/toy_counts.tsv \
  --root-cell c0 \
  --expected-order skills/transcriptomics/scanpy-dpt-trajectory-starter/examples/expected_order.txt \
  --summary-out scratch/scanpy-dpt/summary.json

Verification

  • Skill-local tests: python3 -m unittest discover -s skills/transcriptomics/scanpy-dpt-trajectory-starter/tests -p 'test_*.py'
  • Expected summary: the inferred order equals c0..c5 and pseudotime increases monotonically from 0.0 to 1.0

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