Individual skill

clean-data

Use when a clinical CSV/Excel dataset needs profiling and cleaning before analysis (missing values, outliers, duplicates, type mismatches). Profiles, flags and generates cleaning code in three stages, each gated on the researcher's approval. Never auto-cleans.

skills/clean-data/SKILL.md

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License: MIT

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biostatistics Repository topic
claude-code Repository topic
claude-skills Repository topic
clinical-research Repository topic
diagnostic-accuracy Repository topic
literature-review Repository topic
manuscript Repository topic
medical-ai Repository topic
medical-research Repository topic
meta-analysis Repository topic
data Derived category

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SKILL.mdcore · 8,063 bytes
references/cleaning_patterns.mddoc · 11,864 bytes
references/implausible_value_rules.mddoc · 6,955 bytes
references/profiling_template.pyruns · 11,413 bytes
scripts/check_reverse_coding.pyruns · 7,828 bytes
scripts/check_structural_zero.pyruns · 7,821 bytes
skill.ymlasset · 1,310 bytes
tests/fixtures/profile_na_tokens.csvasset · 190 bytes
tests/fixtures/scale_reverse.csvasset · 133 bytes
tests/fixtures/smoking.csvasset · 103 bytes
tests/fixtures/smoking_clean.csvasset · 91 bytes
tests/fixtures/smoking_sentinel.csvasset · 103 bytes
tests/test_profiling_template.shruns · 2,373 bytes
tests/test_reverse_coding.shruns · 2,502 bytes
tests/test_structural_zero.shruns · 3,629 bytes

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# Data Profiling and Cleaning Skill

Profile, flag, and generate cleaning code for a clinical dataset in three stages, each ending at a
user-approval gate. You generate code and reports; you do NOT auto-clean data. Every cleaning decision
needs the researcher's explicit confirmation, because clinical cleaning calls need domain knowledge.

**PHI first.** If the dataset contains PHI or PII, run `/deidentify` before proceeding, and use
`*_deidentified.*` files when they exist in the working directory. Otherwise work from the data
dictionary / codebook alone, or in a local-only environment with no network access. The skill writes
code that runs on the data; it does not need to see the raw rows to write it.

## Three-Stage Workflow

### Stage 1: Profiling