scRNA-seq Analysis Copilot

A single cell sequencing data analysis interactive helper. Learn scRNA-seq Analysis through natural language interaction with AI charbot.

Key Features • How To Use • Limitations • Credits • Related • License

Key Features

• Answering questions with knowledge
  • 9 preloaded papers with 658,018 words were uploaded for retrieval and answer questions related to general ideas, workflow, sequencing technology, annotation, and mitochondrial genes.
• Single cell sequencing analysis workflow
  • The copilot is capable of loading datasets from given direct url links, process them with API R functions on the server end.
• Graph demonstration
  • The copilot shows generated plots to the users directly.

How To Use

This application is supported by and published on Dify platform. Users might access the agent via Ready-to-use AI WebApp. To clone and run this application, you'll need Dify for GPT agent and R for writing R code and build API installed on your server.

Part One. Build your server

1. Connect to your server through SSH applications like PuTTY.
2. Enter command lines on your server:

# Clone this repository
$ git clone https://github.com/Gina727/scRNA-seq-analyst.git

# Go into the repository
$ cd scRNA-seq-analyst

2. Build the image of app-api

$ docker build -t new-api .
$ docker compose up -d

You may use $ docker ps to check for running containers. 3. Add /rds and /images folders

$ mkdir /scRNA-seq-analyst/app-api/rds
$ mkdir /scRNA-seq-analyst/app-api/images

4. Open "http://your-server's-address:8000/openapi.json"
5. Copy the content of the webpage.

Part Two. Build your agent

1. Register on Dify
2. Create an agent
3. Enter the prompt from this repository: https://github.com/Gina727/scRNA-seq-analyst/blob/main/prompt.txt
4. Load papers in .pdf file from the knowledge list: https://github.com/Gina727/scRNA-seq-analyst/blob/main/knowledge_list.txt to the "Knowledge" section.
5. Go to Tools section. Create new API tools by pasting the openapi.json in the corresponding section.
6. Done!

You may edit the "new_api.R" R script to add new functions.

Limitations

Despite the potential of the agent, it is undeniable that this agent has some limitations. Uploading the files is restricted to using url and there are less function to choose from. So far, the Dify platform does not allow users to directly upload their files in the chat. This may increase inconvenience when using this platform to perform analysis. Additionally, the agent sometimes misunderstood the commands of the user, inhibiting the ease of use.

Credits

This software uses the following open source packages:

• Plumber
• Seurat
• Seurat Data
• ScType

License

Copyright (c) 2024 Author

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.