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Python-based Illumina methylation array processing and analysis software composite package

Project 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

Data Processing

processing pipeline

Quality Control

methylcheck pipeline

Installation

This all-in-one command will install all three packages and their required dependencies.

pip3 install methylsuite

This command was tested in a naive minimal conda environment, created thusly:

conda create -n testsuite

Afterwards, I had to install statsmodels using conda apart from the other dependencies, like so:

conda install statsmodels
pip3 install methylsuite

(Statsmodels uses additional C-compilers during installation)

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