Spatial Trajectory

What it does

When your agent uses it

• Tasks that involve Bioinformatics

Example prompts

• “/spatial-trajectory”

Requirements

• Python 3

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

1. 1Load AnnData (--input) or build a demo. Auto-detect --cluster-key from candidates if not passed.
2. 2Pick / pin root cell: --root-cell or auto-pick via expression-rank; write uns["iroot"] (_lib/trajectory.py:273).
3. 3Run chosen backend
4. 4Compute trajectory genes (correlation with pseudotime) + cluster-mean / median pseudotime summary.
5. 5Render embedding / spatial / diffmap / fate / gene-trend plots.
6. 6Save tables + processed.h5ad + report.

What it can do on your machine

Read from SKILL.md and the folder at commit 6fbd79f. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships script files (Python and R), which the agent can run.

  Shell commands in SKILL.md call:

  • python

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md.

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Spatial Trajectory loads about 1.8k tokens when it runs, and up to ~5.6k if it reads all its reference files. Until then it costs about 100 tokens; SKILL.md has 449 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~100

When it runs · the whole SKILL.md, loaded when a task matches

~1.8k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~5.6k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from TianGzlab/OmicsClaw at commit 6fbd79f, republished under its MIT licence (© TianGzlab). 449 words, ~1,771 tokens.

name

spatial-trajectory

description

Load when inferring pseudotime / lineage trajectories on a preprocessed spatial AnnData via DPT (default — diffusion pseudotime), CellRank (terminal-state + fate-probability), or Palantir (waypoint branch probabilities). Skip when the data has spliced/unspliced layers and you want velocity-driven dynamics (use spatial-velocity); non-spatial scRNA pseudotime (use sc-pseudotime).

version

0.5.0

author

OmicsClaw

license

MIT

emoji

🛤️

tags

spatial, trajectory, pseudotime, dpt, cellrank, palantir, lineage

requires

anndata, cellrank, matplotlib, numpy, palantir, pandas, scanpy, scipy, scvelo, seaborn, statsmodels

<!-- AUTO-GENERATED from skill.yaml (interface) — do not edit by hand. Regenerate: python scripts/generate_skill_md.py <skill_dir> -->

# Demo
python omicsclaw.py run spatial-trajectory --demo --output /tmp/traj_demo

# DPT (default)
python omicsclaw.py run spatial-trajectory \
  --input preprocessed.h5ad --output results/ \
  --method dpt --cluster-key leiden --dpt-n-dcs 10

# CellRank with explicit root cell
python omicsclaw.py run spatial-trajectory \
  --input preprocessed.h5ad --output results/ \
  --method cellrank --root-cell BARCODE_42 \
  --cellrank-n-states 5 --cellrank-frac-to-keep 0.3

# Palantir
python omicsclaw.py run spatial-trajectory \
  --input preprocessed.h5ad --output results/ \
  --method palantir --palantir-num-waypoints 1200 --palantir-knn 30

© TianGzlab, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 8 other files (references) in skills/spatial/spatial-trajectory of TianGzlab/OmicsClaw.

• SKILL.md
• r_visualization/README.md
• r_visualization/trajectory_publication_template.R
• references/methodology.md
• references/output_contract.md
• references/parameters.md
• skill.yaml
• spatial_trajectory.py
• tests/test_spatial_trajectory.py

Open the folder on GitHubat commit 6fbd79f