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CF spatial-transcriptomics-tutorials-with-omicverse

Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq datasets.

FreedomIntelligence/OpenClaw-Medical-Skills Agent Skills author: FreedomIntelligence 2 files body ≈ 3 587 tokens Open the sourcegithub.com↗ analyzed 14 h ago

Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium…

As a process F 33/100 · No process to follow — References files that are not bundled: ../../omicverse_guide/docs/Tutorials-space/, ../../omicverse_guide/docs/Tutorials-space/t_crop_rotate.ipynb, ../../omicverse_guide/docs/Tutorials-space/t_cellpose.ipynb

ProcedureLearningtype and topics are labelled automatically from the skill text
Runs in: Claude / Claude Code ChatGPT / Codex Gemini CLI Cursor GitHub Copilot / VS Code Qwen Code Kimi Code CLI Z.ai (GLM) DeepSeek (Deep Code) Mistral Vibe LangChain (deepagents) OpenClaw Goose OpenCode
JSON
Technical rating
C
83/100
safety, quality, tests
Safety 60%
99
Quality 40%
59
Run on models
none yet
Process rating
F
33/100
No process to follow
References files that are not bundled: ../../omicverse_guide/docs/Tutorials-space/, ../../omicverse_guide/docs/Tutorials-space/t_crop_rotate.ipynb, ../../omicverse_guide/docs/Tutorials-space/t_cellpose.ipynb
Tools and files w 18
0
Result and completion w 14
0
Inputs and preconditions w 11
0
the three weakest of ten parameters · all ten

How to improve

  1. Say in the description WHEN to use the skill ("use when…", example requests): that is the agent's main cue.
  2. The text references files that are not there: add them or drop the references.
For the model run — optional
  • Your own cases (evals/evals.json, 4–6 real requests with expected answers): the full check would then run those instead of a model-drafted suite.
  • A spec.yaml with trigger phrases and assertions — a behaviour contract for CI; `skilltest init` writes a template.

Guard findings · 1

✓ No critical or high findings

Medium and low: 1
  • low Secrets in code secret-high-entropy-token reference.md:9
    High-entropy token-like string (may be an id, hash or a credential) (quoted — discussed, not commanded)
    adata = sc.datasets.visium_sge(sample_id="V1_B…n_1")
    quoted

Files scanned: 2. Evidence is masked. Grey chips explain why severity was lowered.

Against the Agent Skills spec

  • warning description-no-when description does not say WHEN to use the skill (no "use when")
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-space/
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-space/t_crop_rotate.ipynb
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-space/t_cellpose.ipynb
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-space/t_decov.ipynb
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-space/t_starfysh.ipynb
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-space/t_cluster_space.ipynb
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-space/t_staligner.ipynb
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-space/t_spaceflow.ipynb
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-space/t_commot_flowsig.ipynb
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-space/t_gaston.ipynb
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-space/t_slat.ipynb
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-space/t_stt.ipynb
  • note frontmatter-key unknown frontmatter key "title"

Process rating: all ten parameters 33/100

Will not run. References files that are not bundled: ../../omicverse_guide/docs/Tutorials-space/, ../../omicverse_guide/docs/Tutorials-space/t_crop_rotate.ipynb, ../../omicverse_guide/docs/Tutorials-space/t_cellpose.ipynb
  • 0Tools and files. 12 referenced file(s) missing: ../../omicverse_guide/docs/Tutorials-space/, ../../omicverse_guide/docs/Tutorials-space/t_crop_rotate.ipynb, ../../omicverse_guide/docs/Tutorials-space/t_cellpose.ipynb
  • 0Result and completion. Does not say what the result is
  • 0Inputs and preconditions. Does not say what the process needs to start
  • 0Progress reporting. Says nothing while it works
  • 20When it triggers. No condition that starts the skill
  • 30Running it twice. 1 mutating operations with no state check
  • 40Consistency. Frontmatter name (spatial-transcriptomics-tutorials-with-omicverse) differs from the folder (spatial-tutorials)
  • 50Failures and branches. 0 branches, has a failure section
  • 100Steps. 56 steps
  • 100Execution cost. Instruction body is 3587 tokens

Everything here is measured from the skill text rather than judged by a model, so the numbers are checkable. A parameter weighs more when it is a more common reason for the process to stall.

Quality signals

  • +5Description has no quoted example phrases that should trigger the skill
  • +4Description does not say when NOT to use the skill (false activations)
  • +3Output format is not stated: the model decides each time
  • +1No license
  • +2Single-language instructions
  • +3Description length 201: enough signal without eating the budget
  • +4Structure: 11 headings
  • +3Step-by-step instructions: 56 items
  • +4Has examples (0 code blocks)

Quality base 70; lint remarks subtract, signals add up to 100. Result: 59.