Rnaseq De

What it does

When your agent uses it

• Tasks that involve Bioinformatics

Example prompts

• “/rnaseq-de”

Requirements

• Python 3

Workflow steps

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

1. 1Input validation for count matrix and sample metadata
2. 2Pre-DE QC (library size, detected genes, low-count filtering)
3. 3PCA visualisation on normalized expression
4. 4Differential expression from formula + contrast
5. 5Volcano and MA plots
6. 6Markdown report with reproducibility files

What it can do on your machine

Read from SKILL.md and the folder at commit dece754. 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), 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

Rnaseq De loads about 565 tokens when it runs. Until then it costs about 32 tokens; SKILL.md has 112 words of instructions outside code blocks.

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

~32

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

~565

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 dece754, republished under its MIT licence (© ClawBio). 112 words, ~565 tokens.

name

rnaseq-de

description

Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.

license

MIT

metadata.version

0.1.0

metadata.tags

rna-seq, differential expression, bulk, pseudo-bulk, transcriptomics, DESeq2, PyDESeq2, QC, PCA

rnaseq_de_report/
├── report.md
├── result.json
├── figures/
│   ├── pca.png
│   ├── volcano.png
│   └── ma_plot.png
├── tables/
│   ├── qc_summary.csv
│   ├── normalized_counts.csv
│   └── de_results.csv
└── reproducibility/
    ├── commands.sh
    ├── environment.yml
    └── checksums.sha256

python rnaseq_de.py \
  --counts counts.csv \
  --metadata metadata.csv \
  --formula "~ batch + condition" \
  --contrast "condition,treated,control" \
  --output report_dir

© 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

SKILL.md and 6 other files in skills/rnaseq-de of ClawBio/ClawBio.

• SKILL.md
• examples/demo_counts.csv
• examples/demo_metadata.csv
• rnaseq_de.py
• tests/fixtures/pseudobulk_counts.csv
• tests/fixtures/pseudobulk_metadata.csv
• tests/test_rnaseq_de.py

Open the folder on GitHubat commit dece754

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/rnaseq-de