Scrna Embedding

What it does

When your agent uses it

• Tasks that involve Bioinformatics
• Tasks that involve Embeddings

Example prompts

• “/scrna-embedding”

Requirements

• Python 3

Workflow steps

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

1. 1Raw-count Input Validation: Accept raw-count .h5ad and 10x Matrix Market input; reject processed-like matrices.
2. 2scVI/scANVI Latent Embedding: Train scvi.model.SCVI or refine with scvi.model.SCANVI using explicit labels.
3. 3Latent Output Generation: Run neighbors and UMAP from X_scvi, and export latent coordinates.
4. 4Integration Diagnostics: Export lightweight batch-mixing metrics when --batch-key is provided.
5. 5Integrated Export: Save integrated.h5ad with obsm["X_scvi"], log-normalized X, and raw counts in layers["counts"].
6. 6Reproducibility Bundle: Emit commands.sh, environment.yml, and checksums.

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):

  • docs.scvi-tools.org
  • scanpy.readthedocs.io
  • anndata.readthedocs.io

  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

Scrna Embedding loads about 2k tokens when it runs. Until then it costs about 54 tokens; SKILL.md has 633 words of instructions outside code blocks.

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

~54

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). 633 words, ~2,011 tokens.

name

scrna-embedding

description

Local scVI/scANVI-based single-cell latent embedding and batch-aware integration from raw-count .h5ad or 10x Matrix Market input, with stable integrated AnnData export for downstream latent analysis.

license

MIT

metadata.version

0.1.0

metadata.author

Yonghao Zhao

metadata.tags

scrna, single-cell, scvi, scanvi, embedding, integration, batch-correction, h5ad, 10x

# Standard usage
python skills/scrna-embedding/scrna_embedding.py \
  --input <input.h5ad> --output <report_dir>

# Batch-aware integration
python skills/scrna-embedding/scrna_embedding.py \
  --input <input.h5ad> --output <report_dir> \
  --batch-key sample_id

# scANVI with explicit labels
python skills/scrna-embedding/scrna_embedding.py \
  --input <input.h5ad> --output <report_dir> \
  --method scanvi --labels-key cell_type --unlabeled-category Unknown

# 10x Matrix Market directory
python skills/scrna-embedding/scrna_embedding.py \
  --input <filtered_feature_bc_matrix_dir> --output <report_dir>

# Demo mode
python skills/scrna-embedding/scrna_embedding.py \
  --demo --output <report_dir>

# Via ClawBio runner
python clawbio.py run scrna-embedding --input <input.h5ad> --output <report_dir>
python clawbio.py run scrna-embedding --demo

python clawbio.py run scrna-embedding --demo
python clawbio.py run scrna-embedding --demo --batch-key demo_batch

output_directory/
├── report.md
├── result.json
├── integrated.h5ad
├── figures/
│   ├── umap_scvi_latent.png
│   └── umap_scvi_batch.png           # only when batch integration is enabled
├── tables/
│   ├── latent_embeddings.csv
│   └── batch_mixing_metrics.csv      # only when batch integration is enabled
└── 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 2 other files in skills/scrna-embedding of ClawBio/ClawBio.

• SKILL.md
• scrna_embedding.py
• tests/test_scrna_embedding.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/scrna-embedding