cartapa-dataset-checker
CommunityQuality-check CartaPA spatial datasets.
Data & Analytics#embeddings#h5ad#dataset-validation#spatial-proteomics#cartapa#celltype-annotations#coordinate-validation
AuthorKang-chen
Version1.0.0
Installs0
System Documentation
What problem does it solve?
CartaPA dataset checker identifies and reports structural, annotation, and quality issues in spatial proteomics datasets prepared for CartaPA, preventing model misconfiguration and downstream errors.
Core Features & Use Cases
- Validates basic structure, required metadata, and protein marker counts.
- Checks spatial coordinates, celltype annotations, and treatment labels with dataset-specific caveats.
- Generates a concise validation report and optional coordinate visualization for quick quality checks across CODEX-HCC, CODEX-TNBC, IMC-TNBC, SAFE-HNSCC datasets.
Quick Start
Run the dataset checker on your h5ad file using the provided Python script.
Dependency Matrix
Required Modules
numpypandasanndatamatplotlib
Components
scripts
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: cartapa-dataset-checker Download link: https://github.com/Kang-chen/cartabio-ide-config/archive/main.zip#cartapa-dataset-checker Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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