SKILLEMALL.ai
GitHub ↗ RU Sign in

CF bulk-rna-seq-deseq2-analysis-with-omicverse

Walk Claude through PyDESeq2-based differential expression, including ID mapping, DE testing, fold-change thresholding, and enrichment visualisation.

FreedomIntelligence/OpenClaw-Medical-Skills Agent Skills author: FreedomIntelligence 2 files body ≈ 853 tokens Open the sourcegithub.com↗ analyzed 14 h ago

Walk Claude through PyDESeq2-based differential expression, including ID mapping, DE testing, fold-change thresholding, and enrichment visualisation.

As a process F 30/100 · No process to follow — References files that are not bundled: ../../omicverse_guide/docs/Tutorials-bulk/t_deseq2.ipynb, ../../sample/counts.txt

AnalyzerAI and agentsLearningtype 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
85/100
safety, quality, tests
Safety 60%
100
Quality 40%
62
Run on models
none yet
Process rating
F
30/100
No process to follow
References files that are not bundled: ../../omicverse_guide/docs/Tutorials-bulk/t_deseq2.ipynb, ../../sample/counts.txt
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 · 0

✓ No critical or high findings

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-bulk/t_deseq2.ipynb
  • warning missing-ref reference to a missing file: ../../sample/counts.txt
  • note frontmatter-key unknown frontmatter key "title"

Process rating: all ten parameters 30/100

Will not run. References files that are not bundled: ../../omicverse_guide/docs/Tutorials-bulk/t_deseq2.ipynb, ../../sample/counts.txt
  • 0Tools and files. 2 referenced file(s) missing: ../../omicverse_guide/docs/Tutorials-bulk/t_deseq2.ipynb, ../../sample/counts.txt
  • 0Result and completion. Does not say what the result is
  • 0Inputs and preconditions. Does not say what the process needs to start
  • 0Failures and branches. Linear process with no failure handling
  • 20When it triggers. No condition that starts the skill
  • 30Running it twice. 3 mutating operations with no state check
  • 40Consistency. Frontmatter name (bulk-rna-seq-deseq2-analysis-with-omicverse) differs from the folder (bulk-deseq2-analysis)
  • 100Steps. 34 steps
  • 100Execution cost. Instruction body is 853 tokens
  • 100Progress reporting. Reports progress

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 149: enough signal without eating the budget
  • +4Structure: 5 headings
  • +3Step-by-step instructions: 34 items
  • +4Has examples (0 code blocks)

Quality base 70; lint remarks subtract, signals add up to 100. Result: 62.