Welcome to BrainDataPortal Docs!¶
BrainDataPortal is a comprehensive platform for single-cell, spatial transcriptomics, and other omics data visualization and exploration. This documentation will guide you through the installation and data preparation processes.
Overview¶
- This is project designed for the brain multi-modal data visualization and exploration.
- The supported assays include: scRNAseq, scATACseq, Visium Spatial Transcriptomics, xQTL, GWAS.
- The backend is running on FastAPI and uvicorn.
- The frontend is built with React and Vite.
- The data is stored in SQLite3 and JSON files.
- Use zustand for state management, and Material UI for web page layout design
Directory structure¶
BrainDataPortal/
|-- Backend/
| |-- main.py ## The main entry of the backend
| |-- db.py ## The database connection and management
| |-- settings.py ## The configuration of the backend
| |-- requirements.txt ## The required libraries of the backend
| |-- funcs/ ## This folder contains request handler functions of the backend
| | |-- get_data.py ## The request handler functions for data
| | |-- utils.py ## The utils functions
| | `-- ...
| |-- models/ ## This folder contains database models of the backend
| | |-- dataset.py ## The dataset model/table
| | `-- ...
| |-- routes/ ## This folder contains routes endpoints of requests
| | |-- api_routes.py
| | |-- qtl_routes.py
| | |-- visium_routes.py
| | `-- ...
| |-- SampleSheets/ ## Upload sample sheets here when adding new datasets
| | |-- Sample_snRNAseq.csv
| | `-- ...
| |-- datasets/ ## The datasets are stored here
| | |-- dataset_1/
| | | |-- meta_cell.json
| | | |-- meta_sample.json
| | | |-- ...
| | `-- ...
| |-- bdp_db.db ## The database file
| `-- ...
|-- Frontend
| |-- index.html ## The entry page of the frontend
| |-- vite.config.js ## The vite configuration file
| |-- package.json ## The dependencies and dev/build settings of the frontend
| |-- env/ ## The environment variables
| | |-- .env ## The global environment variables
| | |-- .env.development ## The development environment variables
| | `-- .env.production ## The production environment variables
| |-- src/ ## The source code of the frontend
| | |-- App.jsx ## Define the routes of the frontend
| | |-- index.css ## The global styles of the frontend
| | |-- main.jsx ## The entry file of the frontend
| | |-- components/ ## The components of the frontend
| | | `-- ...
| | |-- pages/ ## The pages of the frontend
| | | `-- ...
| | |-- utils/ ## The fucntional utils
| | | `-- ...
| | |-- store/ ## The stores for state management
| | |-- api/ ## The api for data fetching
| | `-- ...
| `-- ...
`-- README.md