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

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