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🧬 scRNA Embedding · clawbio | DecimalAI

scienceby clawbio

🧬 scRNA Embedding

clawbio/scrna-embedding

Source clawbio/clawbio ↗License MIT

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.

SkillScore100Maintained

Automatic

Research pack

Last verified 8/16/2026

What it changes

Passed 20 of 20 test cases with the skill, and 5 of 20 without it.

Without skill23%

With skill100%

Checks it passed that the model alone missed

Passes --output with the output path.
Includes report.md in output directory.
Includes --method scanvi in the command.

and 31 more in the full report

17 fixed5 passed either way0 still failing0 broke

Pass-rate lift: +77 pp
Tokens: +28%
Agent turns: 0%
Response time: -62%

Model gemini-3.6-flashMeasured 8/16/2026v122 of 22 cases passed with skill · 20 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/clawbio-scrna-embedding/SKILL.md https://app.decimal.ai/s/clawbio-scrna-embedding/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add clawbio-scrna-embedding, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/clawbio-scrna-embedding/ and pins it in .decimal/skills.lock

decimalai skills add clawbio-scrna-embedding

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/clawbio-scrna-embedding/SKILL.md https://app.decimal.ai/s/clawbio-scrna-embedding/SKILL.md

Raw file: /s/clawbio-scrna-embedding/SKILL.md ↗ · machine-readable summary at /s/clawbio-scrna-embedding.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 15 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 15

Prompt

Write the exact CLI command to run batch-aware scVI integration on `donor_data.h5ad` where the batch covariate is stored in column `donor_id`, saving results to `results_dir/`.

What was checked, without and with the skill
Checked	Without skill	With skill
Includes --batch-key donor_id in the CLI arguments.	Missed	Passed
Includes --input donor_data.h5ad in the CLI arguments.	Missed	Passed
Includes --output results_dir in the CLI arguments.	Missed	Passed

case-08 · gemini-3.6-flash · 8/16/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md171 linessingle file

🧬 scRNA Embedding

You are scRNA Embedding, a specialised ClawBio agent for local single-cell latent embedding and batch-aware integration with scVI/scANVI.

Why This Exists

Single-cell datasets often need a model-based latent representation instead of a purely Scanpy-native PCA workflow.

Without it: Users manually wire together scvi-tools training, latent export, downstream handoff, and report generation.
With it: One command trains scVI/scANVI locally, writes X_scvi, saves a stable integrated.h5ad, and hands off cleanly to scrna-orchestrator for downstream clustering, annotation, and contrastive markers.
Why ClawBio: The workflow stays local-first, preserves reproducibility outputs, and keeps the standard report.md / result.json contract.

Core Capabilities

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

Input Formats

Format	Extension	Required Fields	Example
AnnData raw counts	`.h5ad`	Raw count matrix in `X` or a selected counts `layer`; cell metadata in `obs`; gene metadata in `var`	`pbmc_raw.h5ad`
10x Matrix Market	directory, `.mtx`, `.mtx.gz`	`matrix.mtx(.gz)` plus matching `barcodes.tsv(.gz)` and `features.tsv(.gz)` or `genes.tsv(.gz)`	`filtered_feature_bc_matrix/`
Demo mode	n/a	none	`python clawbio.py run scrna-embedding --demo`

Workflow

When the user asks for scVI/scANVI embedding, latent integration, or batch correction:

Validate: Check raw-count .h5ad / 10x input (or --demo) and reject processed-like matrices.
Filter: Apply basic QC thresholds for genes, cells, and mitochondrial fraction.
Train: Fit scvi.model.SCVI on HVG raw counts, optionally using --batch-key, and refine with scvi.model.SCANVI when --method scanvi plus explicit labels are provided.
Project: Export X_scvi, run latent-space neighbors and UMAP.
Generate: Write a minimal report.md, result.json, integrated.h5ad, latent tables, figures, and reproducibility files, plus the recommended downstream scrna command.

CLI Reference

Track record

Benchmark

20 / 20

test cases passed, vs 5 / 20 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

clawbio / clawbio

skills/scrna-embedding/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1

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See it in action

What's inside

🧬 scRNA Embedding

Why This Exists

Core Capabilities

Input Formats

Workflow

CLI Reference

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

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