single-cell-foundation-model-geneformer
CommunityOrchestrate Geneformer workflows.
Data & Analytics#embeddings#classification#single-cell#tokenization#scRNA-seq#perturbation#geneformer
AuthorPharMolix
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Geneformer workflows for single-cell data processing are complex and time-consuming; this skill provides structured guidance to tokenize raw data, classify cells, extract embeddings, and perform in silico perturbations.
Core Features & Use Cases
- Tokenization with TranscriptomeTokenizer to create tokenized .dataset objects for downstream tasks
- Classification and embedding extraction using Geneformer components like Classifier and EmbExtractor
- In silico perturbation analyses to simulate state changes and explore perturbations in silico
Quick Start
Tokenize raw scRNA-seq data with TranscriptomeTokenizer to prepare tokenized datasets for downstream classification, embedding extraction, and perturbation workflows.
Dependency Matrix
Required Modules
None requiredComponents
references
💻 Claude Code Installation
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Please help me install this Skill: Name: single-cell-foundation-model-geneformer Download link: https://github.com/PharMolix/OpenBioMed/archive/main.zip#single-cell-foundation-model-geneformer Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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