Metadata-Version: 2.1
Name: GeneCluster
Version: 0.1.0
Summary: A gene clustering model using deep learning
Home-page: https://github.com/Byting820/GeneCluster
Author: Byting
Author-email: yutingya820@163.com
License: UNKNOWN
Description: # GeneCluster
        
        GeneCluster, a gene clustering method for Single Cell RNA-seq data.
        
        ## Requirements
        python --- 3.8.10
        
        scanpy --- 1.8.2
        
        umap-learn --- 0.5.3
        
        torch --- 1.8.1
        
        torchvision --- 0.9.1
        
        faiss-gpu --- 1.7.1
        
        ## Usage
        The raw single-cell data in h5 format first goes through DataProcess.py to get the gene-cell in csv format, and the csv format is fed into the model for training.
        
        ```bash
        # Run main.py directly with specified parameters
        python main.py --nmb_cluster 20 --batch 128 --epochs 100 \
                       --lr 0.01 --data_path normal_data.csv \
                       --ckpt_path train_res &
        
        # Alternatively, run the GeneCluster package with parameters
        GeneCluster --data_path path/to/dataset.csv --epochs 100 --nmb_cluster 20 --batch 128 --ckpt_path train_res   
        ```
        
        or
        
        ```bash
        sh train.sh
        ```
        
        Please note that the model outputs gene embeddings extracted by training (features.npy), which can be used to predict gene co-expression relationships and identify gene modules.
        
        Here is an example on pbmc3k.h5ad scRNA-seq data.
        
        ## Example
        
        ```python
        from genecluster import main
        
        args = {
            "data_path": "path/to/dataset.csv",
            "epochs": 100,
            "nmb_cluster": 10,
            # other arguments
        }
        
        main(args)
        ```
        
        ## Contact
        
        Yuting Bai (yutingya820@163.com)
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
