Single Cell Analysis Auto

AI-assisted single-cell analysis

Quick Start

1. Install Conda

   If you don’t have Conda installed, please install Miniconda or Anaconda.

2. Clone the repository

   git clone https://github.com/MoleSir/scauto
   cd scauto

3. Create the environment

   Use spec-file.txt to create an exact environment:

   conda create --name my_env --file spec-file.txt

   • Replace my_env with the environment name of your choice.
   • This will install all packages and versions listed in spec-file.txt to ensure reproducibility.

4. Activate the environment

   conda activate my_env

5. Running the project

   python3 main.py

References

SCA

• https://zhuanlan.zhihu.com/p/345403616
• https://github.com/NIH-NEI/SCassist
• https://nih-nei.github.io/SCassist/SCassist-Tutorial-BCRUV.html
• https://github.com/theislab/single-cell-tutorial/
• https://www.sc-best-practices.org/preamble.html
• https://academic.oup.com/bioinformatics/article/41/8/btaf402/8198067
• https://www.embopress.org/doi/full/10.15252/msb.20188746

MCP

• https://scrapfly.io/blog/posts/how-to-build-an-mcp-server-in-python-a-complete-guide

RAG

• https://github.com/weiwill88/Local_Pdf_Chat_RAG.git
• https://zhuanlan.zhihu.com/p/686844517
• https://zhuanlan.zhihu.com/p/29761721645
• github.com/vikparuchuri/marker