https://github.com/vanvalenlab/deepcelltypes-demo-08-2023
Executable demo of deepcelltypes model pipeline
https://github.com/vanvalenlab/deepcelltypes-demo-08-2023
Last synced: 30 days ago
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Executable demo of deepcelltypes model pipeline
- Host: GitHub
- URL: https://github.com/vanvalenlab/deepcelltypes-demo-08-2023
- Owner: vanvalenlab
- Created: 2023-08-26T02:26:58.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2023-08-26T02:50:05.000Z (almost 3 years ago)
- Last Synced: 2025-01-04T18:31:42.677Z (over 1 year ago)
- Language: Python
- Size: 15.6 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# `deepcelltypes` interactive demo
Cell-type prediction for multiplexed spatial proteomic data.
To run the demo, you will need:
#. Python
#. A running docker daemon
#. The prototype model and example data
## Setup
### Docker
Ensure that your docker daemon is running and doesn't require elevated
permissions:
```bash
docker run hello-world
```
### Python
Create a Python virtual environment and install the necessary dependencies:
```bash
python -m venv demo-env
source demo-env/bin/activate # or whichever script is appropriate for your shell
pip install -r requirements.txt
```
### Model and example data
The model is not (yet) publicly available as it is currently under development.
For access to the demo data and model prototype, direct inquiries to
vanvalenlab@gmail.com.
The model and data should be unpacked in the top-level directory of this
repository:
```bash
tar -xzf demo_data_model.tar.gz
```
## Running the demo
The demo is available in the form of a markdown-based jupyter notebook.
Launch a new session with:
```bash
jupyter notebook
```
Then right-click `presentation.md` and select `Jupytext Notebook` from the
`Open with` menu.