Welcome to BioLLM’s documentation!

Welcome to the documentation for BioLLM, a standardized framework designed to facilitate the integration and application of scFMs in single-cell RNA sequencing analyses.

Getting Started:

• Introduction
• Installation

Tutorials:

• BioLLM: Cell Embedding Generation from scFM Models (Zero-Shot) Task
• BioLLM: Gene Regulatory Network (GRN) Task
• BioLLM: CellType Annotation
• BioLLM: DrugSensitivity Task
• Integration of Novel Models into the BioLLM Framework: A Step-by-Step Guide

API Reference:

• Base Modules
  • biollm.tasks.bio_task
  • biollm.loader.load_llm
  • biollm.loader.scbert
  • biollm.loader.scfoundation
  • biollm.loader.scgpt
  • biollm.loader.geneformer
  • biollm.loader.cellplm

Release:

• Release Notes
  • Changelog

References:

• Download Links for Pre-trained Models and Gene Vocabulary