Diff Visualizer

What it does

When your agent uses it

• Tasks that involve Bioinformatics

Example prompts

• “/diff-visualizer”

Requirements

• Python 3

Workflow steps

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

1. 1Auto-detect upstream outputs from rnaseq-de, scrna-orchestrator, or direct DE/marker tables.
2. 2Bulk RNA visualisation with volcano, MA, top-gene bars, and optional counts+metadata heatmaps.
3. 3scRNA visualisation with dataset-level contrast volcanoes, within-cluster comparison panels, marker ranking bars, and optional…
4. 4Reporting with report.md, self-contained report.html, result.json, and reproducibility files.

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

  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

  Links to these hosts (documentation or services it may open):

  • scanpy.readthedocs.io
  • matplotlib.org

  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

Diff Visualizer loads about 1.6k tokens when it runs. Until then it costs about 34 tokens; SKILL.md has 416 words of instructions outside code blocks.

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

~34

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

~1.6k

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). 416 words, ~1,575 tokens.

name

diff-visualizer

description

Rich downstream visualisation and reporting for bulk RNA-seq differential expression and scRNA marker/contrast outputs.

license

MIT

metadata.version

0.1.0

metadata.author

Yonghao Zhao

metadata.tags

differential-expression, visualisation, rnaseq, scrna, volcano, heatmap

# Bulk table
python skills/diff-visualizer/diff_visualizer.py \
  --input de_results.csv --output diffviz_report

# Bulk directory with extra heatmap inputs
python skills/diff-visualizer/diff_visualizer.py \
  --input output/rnaseq_run --counts counts.csv --metadata metadata.csv \
  --output diffviz_report

# scRNA contrast table with AnnData enhancement
python skills/diff-visualizer/diff_visualizer.py \
  --mode scrna --input contrastive_markers_full.csv --adata cells.h5ad \
  --output diffviz_report

# Demo
python skills/diff-visualizer/diff_visualizer.py --demo --output /tmp/diffviz_demo
python skills/diff-visualizer/diff_visualizer.py --demo --mode scrna --output /tmp/diffviz_scrna_demo

# Via ClawBio runner
python clawbio.py run diffviz --input de_results.csv --output diffviz_report
python clawbio.py run diffviz --demo

python clawbio.py run diffviz --demo
python clawbio.py run diffviz --demo --mode scrna

output_directory/
├── report.md
├── report.html
├── result.json
├── figures/
│   ├── volcano.png
│   ├── top_genes_bar.png
│   ├── ma_plot.png
│   ├── top_genes_heatmap.png
│   ├── contrast_volcano.png
│   ├── top_markers_bar.png
│   ├── marker_rank_bars.png
│   ├── marker_dotplot.png
│   ├── marker_heatmap.png
│   └── umap_feature_panel.png
├── tables/
│   ├── top_genes.csv
│   ├── significant_genes.csv
│   ├── top_markers.csv
│   └── top_markers_by_cluster.csv
└── reproducibility/
    ├── commands.sh
    ├── environment.yml
    └── checksums.sha256

© 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 7 other files in skills/diff-visualizer of ClawBio/ClawBio.

• SKILL.md
• diff_visualizer.py
• examples/demo_bulk_counts.csv
• examples/demo_bulk_de_results.csv
• examples/demo_bulk_metadata.csv
• examples/demo_scrna_contrast.csv
• examples/demo_scrna_markers.csv
• tests/test_diff_visualizer.py

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/diff-visualizer