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BC bio-de-deseq2-basics

Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold change shrinkage. Use when performing DE analysis with DESeq2.

FreedomIntelligence/OpenClaw-Medical-Skills Agent Skills author: FreedomIntelligence 5 files body ≈ 2 723 tokens Open the sourcegithub.com↗ analyzed 14 h ago

Perform differential expression analysis using DESeq2 in R/Bioconductor.

As a process C 58/100 · Has gaps — weak spots: result and completion, when it triggers, inputs and preconditions

AnalyzerWriting and documentsData and analyticsInfrastructuretype 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
B
93/100
safety, quality, tests
Safety 60%
100
Quality 40%
82
Run on models
none yet
Process rating
C
58/100
Has gaps
Result and completion w 14
0
Inputs and preconditions w 11
0
When it triggers w 12
20
the three weakest of ten parameters · all ten

How to improve

    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

    • note frontmatter-key unknown frontmatter key "tool_type"
    • note frontmatter-key unknown frontmatter key "primary_tool"
    • note edit-residue the text marks something as outdated (lines 335, 340): check that old rules are not kept next to new ones — the full check reads the text for contradictions

    Process rating: all ten parameters 58/100

    • 0Result and completion. Does not say what the result is
    • 0Inputs and preconditions. Does not say what the process needs to start
    • 20When it triggers. No condition that starts the skill
    • 30Running it twice. 4 mutating operations with no state check
    • 50Failures and branches. 0 branches, has a failure section
    • 100Tools and files. No external tools needed
    • 100Steps. 4 steps
    • 100Consistency. Name and required fields are in place
    • 100Execution cost. Instruction body is 2723 tokens
    • 100Progress reporting. Reports progress
    • low 22 top-level sections: this looks like several domains in one skill

    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 269: enough signal without eating the budget
    • +4Structure: 26 headings
    • +3Step-by-step instructions: 4 items
    • +4Has examples (19 code blocks)

    Quality base 70; lint remarks subtract, signals add up to 100. Result: 82.