Metadata-Version: 2.1
Name: methylsuite
Version: 1.0.2
Summary: Python-based Illumina methylation array processing and analysis software composite package
Home-page: https://life-epigenetics-methylprep.readthedocs-hosted.com/en/latest/
Author: FOXO Bioscience
Author-email: info@FOXOBioScience.com
License: MIT
Project-URL: Funding, https://FOXOBioScience.com/
Description: ## Overview
        
        This meta package will install the python packages that together make up the `methylsuite`:
        
        - `methylprep` is a python package for processing DNA methylation data from Illumina arrays. It provides:
            - A variety of background subtraction and normalization methods found in similar R-based packages.
            - Support for Illumina arrays (27k, 450k, EPIC, mouse).
            - Support for analyzing public data sets from GEO (the NIH Gene Expression Omnibus is a database) .
            - Support for managing data in `Pandas` DataFrames.
        - `methylcheck` includes:
           - quality control (QC) functions for filtering out unreliable probes, based on the published literature,  sample outlier detection, plots similar to Genome Studio functions, sex prediction, and
           and interactive method for assigning samples to groups, based on array data, in a Jupyter notebook.
        - `methylize` provides these analysis functions:
           - differentially methylated probe statistics (between treatment and control samples).
           - volcano plots (which probes are the most different).
           - manhattan plot (where in genome are the differences).
        
        ### Parts of `methylsuite`
        ![](https://github.com/FOXOBioScience/methylprep/blob/master/docs/methyl-suite.png?raw=true)
        
        ### Data Processing
        ![processing pipeline](https://github.com/FOXOBioScience/methylprep/blob/master/docs/methylprep-processing-pipeline.png?raw=true)
        
        ### Quality Control
        ![methylcheck pipeline](https://raw.githubusercontent.com/FOXOBioScience/methylcheck/master/docs/methylcheck_functions.png)
        
        ## Installation
        
        This all-in-one command will install all three packages and their required dependencies.
        
        ```python
        pip3 install methylsuite
        ```
        
        This command was tested in a naive minimal conda environment, created thusly:
        
        ```python
        conda create -n testsuite
        ```
        
        Afterwards, I had to install `statsmodels` using conda apart from the other dependencies, like so:
        
        ```python
        conda install statsmodels
        pip3 install methylsuite
        ```
        
        (Statsmodels uses additional C-compilers during installation)
        
Keywords: methylation dna data processing epigenetics illumina
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Framework :: Jupyter
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Financial and Insurance Industry
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Description-Content-Type: text/markdown
