https://github.com/kojikoji/deepcolor
https://github.com/kojikoji/deepcolor
Last synced: 22 days ago
JSON representation
- Host: GitHub
- URL: https://github.com/kojikoji/deepcolor
- Owner: kojikoji
- License: mit
- Created: 2022-02-06T09:07:39.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2024-01-02T15:54:06.000Z (over 1 year ago)
- Last Synced: 2024-10-30T13:45:52.387Z (7 months ago)
- Language: Jupyter Notebook
- Size: 384 KB
- Stars: 9
- Watchers: 1
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-cell-cell-communication - DeepCOLOR - [python]- DeepCOLOR is intended to analyze colocalization relation ships between single cell transcriptomes, integrating them with spatial transcriptome. (Uncategorized / Uncategorized)
README
# deepCOLOR: DEEP Generative model for single-cell COLOcalization Representation
DeepCOLOR is intended to analyze colocalization relation ships between single cell transcriptomes, integrating them with spatial transcriptome.
## Instalation
You can install deepCOLOR using pip command from your shell.
```shell
pip install deepcolor imgaug==0.2.5
```
## Usage
You need to prepare [`AnnData` objects](https://anndata.readthedocs.io/en/latest/) which includes raw count matrix of gene expression for single cell and spatial transcriptome respectively. You can see the usage in [IPython Notebook](tutorial/deepcolor_tutorial.ipynb).