Metadata-Version: 2.1
Name: pymethylprocess
Version: 0.1.2
Summary: Preprocessing methylation pipeline, written in python. Easy to use and highly parallelized.
Home-page: https://github.com/Christensen-Lab-Dartmouth/PyMethylProcess
Author: Joshua Levy
Author-email: joshualevy44@berkeley.edu
License: MIT
Description: ## PyMethylProcess
        
        ![pymethylprocess_overview](https://user-images.githubusercontent.com/19698023/54838986-4e152e00-4ca0-11e9-9012-a6d710fffee3.jpeg)
        
        https://github.com/Christensen-Lab-Dartmouth/PyMethylProcess  
        
        Help documentation: https://christensen-lab-dartmouth.github.io/PyMethylProcess/  
        
        Alternatively, you can access the pdf: PyMethylProcess.pdf
        
        What is it:
        * Preprocess 450k and 850k methylation IDAT files in parallel using Minfi, ENmix, and meffil  
        * Convenient and scalable implementation  
        * Imputation and Feature Selection  
        * Preparation for machine learning pipelines    
        
        Why:
        * Make DNAm accessible to python developers and more machine learning oriented researchers  
        * Streamlined analysis makes processing easy  
        
        Getting Started:  
        * Installation:   
            * pip install git+https://github.com/bodono/scs-python.git@bb45c69ce57b1fbb5ab23e02b30549a7e0b801e3 git+https://github.com/jlevy44/hypopt.git@27aefef62483174736bd6d5a1b3983dbaf4184dc
            * pip install pymethylprocess && pymethyl-install_r_dependencies (Note: May need to prefix pip install with MACOSX_DEPLOYMENT_TARGET=10.9 CC=clang CXX=clang++ for Mac OS install)
            * docker pull joshualevy44/pymethylprocess
            * Alternatively, run sh build_docker.sh to build the docker container, and then run sh run_docker.sh to run the docker container.
            * Or see example scripts for usage.
        * Example Usage Scripts (in github repo): Located in ./example_scripts/  
        * Help docs (in github repo): https://christensen-lab-dartmouth.github.io/PyMethylProcess/
        
        *PyMethyProcess* is pending submission and review, and link to paper will be posted shortly.
        
        ![pipeline-download](https://user-images.githubusercontent.com/19698023/54839004-566d6900-4ca0-11e9-97fa-f338d11b896b.jpeg)  
        ![pipeline-format](https://user-images.githubusercontent.com/19698023/54839010-59685980-4ca0-11e9-92da-58bccec68347.jpeg)  
        ![pipeline-preprocess](https://user-images.githubusercontent.com/19698023/54839016-5cfbe080-4ca0-11e9-8c7e-22a871483d16.jpeg)  
        ![pipeline-visualize](https://user-images.githubusercontent.com/19698023/54839038-66854880-4ca0-11e9-8afe-e167806f83ce.jpeg)  
        ![pipeline-train-test-split](https://user-images.githubusercontent.com/19698023/54839060-713fdd80-4ca0-11e9-85a8-9385012a6807.jpeg)  
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
