Metadata-Version: 2.1
Name: SpaDecon
Version: 1.1.1
Summary: SpaDecon: Integrating gene expression and histology information to perform cell type deconvolution on spatial transcriptomics data
Home-page: https://github.com/kylepcoleman87/SpaDecon
Author: Kyle Coleman
Author-email: kylecole@pennmedicine.upenn.edu
License: UNKNOWN
Description: # SpaDecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning
        
        ### Kyle Coleman, Jian Hu, Amelia Schroeder, Edward B. Lee, Mingyao Li*
        
        SpaDecon is a semi-supervised learning-based method developed to perform cell-type deconvolution on spatially resolved transcriptomics (SRT) datasets. SpaDecon has been shown to provide accurate cell-type deconvolution results for both Spatial Transcriptomics (ST) and 10X Visium SRT datasets. Annotated scRNA-seq gene expression data from the same type of tissue as the SRT data are required for deconvolution.
        
        ![png](images/spadecon_workflow.png)
        
        ## SpaDecon Installation
        - SpaDecon installation requires a python version of at least 3.6. The version of python can be checked by: 
        ```python
        import platform
        platform.python_version()
        ```
        
            '3.7.11'
        
        We recommend creating and activating a new conda environment when installing the SpaDecon package. For instance, 
        ```bash
        conda create -n SpaDecon python=3.7
        conda activate SpaDecon
        ```        
            
        There are mulitple ways to install SpaDecon:
            
        - Install SpaDecon using PyPI:
        
        ```bash
        pip3 install SpaDecon   
        ```    
            
        - Download and install SpaDecon package from GitHub: 
        
        ```bash
        git clone https://github.com/kpcoleman/SpaDecon
        cd SpaDecon/
        python3 setup.py install --user
        ```
        
        ## Tutorial
        A markdown tutorial file can be found here: https://github.com/kpcoleman/SpaDecon/blob/main/tutorial/Tutorial.md
        
        A tutorial in the form of a jupyter notebook can be found here: https://github.com/kpcoleman/SpaDecon/blob/main/tutorial/tutorial.ipynb 
        
        
        
        ## Software Requirements  
        python >= 3.6  
        keras==2.2.4  
        pandas==1.2.4  
        numpy==1.20.1  
        scipy==1.6.2  
        scanpy==1.7.0  
        anndata==0.7.6  
        sklearn  
        tensorflow==1.14.0  
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
