De Summary

What it does

When your agent uses it

• Research & Science work in your project

Example prompts

• “/de-summary”

Requirements

• Python 3

Workflow steps

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

1. 1Validate input: Confirm required columns exist (gene identifier, log2FoldChange, padj). Detect column naming variants (adj.P.Val for…
2. 2Apply significance thresholds: Filter genes meeting BOTH criteria: padj < 0.05 AND |log2FoldChange| >= 1.0. Count total significant genes…
3. 3Rank and select top 10: Sort significant genes by padj (ascending). Break ties by |log2FoldChange| (descending). Select top 10 for the…
4. 4Identify biological themes: Group top DE genes by known biological function. Assign each gene to at least one theme from…
5. 5Generate observations: Produce 3 to 5 key observations about the DE landscape: direction bias (more up or down?), dominant functional…
6. 6Check for common pitfalls: Verify that housekeeping genes (GAPDH, ACTB, TUBB) are not in the significant set (if they are, flag as a…
7. 7Report: Generate markdown report with summary statistics, top-10 table, themes, observations, and reproducibility bundle.

What it can do on your machine

Read from SKILL.md and the folder at commit 5e045e3. 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

  No scripts in the folder and no shell commands in SKILL.md (its code samples are json).

  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

De Summary loads about 2k tokens when it runs. Until then it costs about 37 tokens; SKILL.md has 734 words of instructions outside code blocks.

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

~37

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

~2k

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 ClawBio/ClawBio at commit 5e045e3, republished under its MIT licence (© ClawBio). 734 words, ~2,009 tokens.

name

de-summary

description

Summarise pre-computed differential expression results with ranked gene lists, biological themes, and publication-ready interpretation.

license

MIT

metadata.version

0.1.0

metadata.author

Manuel Corpas

metadata.tags

transcriptomics, differential-expression, summary, interpretation, bulk-rna-seq

{
  "summary_statistics": {
    "total_genes_tested": 50,
    "significant_genes": 28,
    "up_regulated": 18,
    "down_regulated": 10,
    "thresholds": {"padj": 0.05, "log2fc_min": 1.0}
  },
  "top_10_genes": [
    {"rank": 1, "gene": "IL6", "log2FC": 3.82, "padj": 1.1e-31, "direction": "up"},
    {"rank": 2, "gene": "CXCL10", "log2FC": 3.45, "padj": 1.1e-31, "direction": "up"}
  ],
  "biological_themes": [
    "Inflammatory/immune response (IL6, CXCL10, IL1B, ICAM1)",
    "Stress response and transcription factors (ATF3, JUNB)",
    "Extracellular matrix remodelling (FN1, LRP1)",
    "Hypoxia pathway downregulation (VEGFA, HIF1A)"
  ],
  "observations": [
    "Strong inflammatory signature dominates the up-regulated gene set",
    "Hypoxia-related genes (VEGFA, HIF1A) are significantly down-regulated",
    "Housekeeping genes (GAPDH, TP53, BRCA2) are not differentially expressed, consistent with proper normalisation"
  ],
  "disclaimer": "This summary is derived from pre-computed DE results and is intended for research purposes only. Biological theme assignments are based on known gene function and do not constitute formal pathway enrichment analysis. Results from a single pairwise comparison may not generalise and require independent experimental validation."
}

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

Files

Just SKILL.md in skills/de-summary of ClawBio/ClawBio.

Open the folder on GitHubat commit 5e045e3

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

• BioTender-max/awesome-bio-agent-skillsskills/clawbio/de-summary