single-cell-foundation-model-scgpt
CommunityRun local scGPT workflows for single-cell data.
Data & Analytics#preprocessing#single-cell#embedding#anndata#reference-mapping#scgpt#vocabulary-matching
AuthorPharMolix
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This skill helps researchers manage and execute local scGPT workflows for preprocessing, vocabulary alignment, cell embedding extraction, and reference mapping in a single-cell analysis project.
Core Features & Use Cases
- Local workflow orchestration: coordinates preprocessing, binning, and embedding steps using the scGPT repo at /DATA/disk0/zhaosy/home/scGPT.
- Vocabulary alignment: matches genes to the local scGPT vocabulary to ensure consistent downstream analysis.
- Tutorial-guided experimentation: supports reference mapping, GRN, and integration tutorials provided by scGPT.
Quick Start
Inspect the local scGPT project and run the recommended preprocessing or embedding workflow from the provided tutorials.
Dependency Matrix
Required Modules
None requiredComponents
references
💻 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: single-cell-foundation-model-scgpt Download link: https://github.com/PharMolix/OpenBioMed/archive/main.zip#single-cell-foundation-model-scgpt Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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