Metadata-Version: 2.1
Name: gbm-org-analysis
Version: 0.0.1
Summary: Extracts and analyzes GBM-organoid data exported from Imaris
Home-page: https://github.com/rybinmj/gbm_org_analysis
Author: Matt Rybin
Author-email: mxr2011@miami.edu
License: UNKNOWN
Description: # gbm_org_analysis
        
        Designed to analyze glioblastoma (GBM) cell and brain organoid data exported from Imaris.
        
        More specifically this package extracts, performs relavent comparative statistics, and generates preliminary figures for the following data: 1) total number of GBM cells; 2) distance of each cell to the nearest surface of the organoid (distance to surface); 3) number of GBM cells whose distace to surface exceeds a defined invasion threshold; 4) brain organoid volume; 5) brain organoid surface area.
        
        ## Installation
        
        ```zsh
        $ pip install gbm_org_analysis
        ```
        
        ## Reproducing experimental analysis with test dataset
        
        1. Set up new virtual environement (if desired)
        
        2. Download and unzip test dataset
        
            ```zsh
            $ curl -L https://miami.box.com/shared/static/uzm30l05xwjhx2v9qeie9ruc12siz00f.zip --output Gbm_TestData.zip
            $ unzip Gbm_TestData.zip
            ```
        
        3. Navigate to data directory and install requirements
        
            ```zsh
            $ cd Gbm_TestData
            $ pip install -r requirements.txt
            ```
        
        4. Run analysis
        
            ```zsh
            $ python3 Analysis/test_analysis.py
            ```
        
        Notes:
        * Step 3: requirements.txt includes instructions for installing gbm_org_analysis package
        * Step 4: test_analysis.py automatically exports processed data, statistical results and preliminary figures to three new sub directories
        * Full datasets will be made available for download as they are published
        
        Compiled code:
        
        ```zsh
        $ curl -L https://miami.box.com/shared/static/uzm30l05xwjhx2v9qeie9ruc12siz00f.zip --output Gbm_TestData.zip
        $ unzip Gbm_TestData.zip
        $ cd Gbm_TestData
        $ pip install -r requirements.txt
        $ python3 Analysis/test_analysis.py
        ```
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
