Use this skill to run a deterministic toy batch-correction pass with Scanpy's ComBat implementation and summarize how much the batch gap shrinks after correction.
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# Scanpy ComBat Batch Correction Starter
Use this skill to run a deterministic toy batch-correction pass with Scanpy's ComBat implementation and summarize how much the batch gap shrinks after correction.
## What it does
- Loads a toy count matrix and per-cell metadata with batch and cell-type labels.
- Builds an AnnData object, normalizes counts, and log-transforms the matrix.
- Runs `scanpy.pp.combat` on the `batch` column.
- Reports pre/post batch mean differences plus retained cell-type separation.
## When to use it
- You need a lightweight verified starter for single-cell batch correction.
- You want a local integration example before moving on to heavier `scvi-tools` workflows.
## Example
```bash
slurm/envs/scanpy/bin/python skills/transcriptomics/scanpy-combat-batch-correction-starter/scripts/run_scanpy_combat_batch_correction.py \
--counts skills/transcriptomics/scanpy-combat-batch-correction-starter/examples/toy_counts.tsv \
--metadata skills/transcriptomics/scanpy-combat-batch-correction-starter/examples/toy_metadata.tsv \
--summary-out scratch/scanpy-combat/summary.json
```
## Verification
- Skill-local tests: `python3 -m unittest discover -s skills/transcriptomics/scanpy-combat-batch-correction-starter/tests -p 'test_*.py'`
- Repository smoke: `python3 -m unittest tests.smoke.test_phase26_frontier_completion_skills -v`
