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

Project description


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 or downloading GEO datasets from NIH. It provides:
    • 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.
    • data cleaning functions during processing, including:
      • infer type-I channel switch
      • NOOB
      • poobah (p-value with out-of-band array hybridization, for filtering lose signal-to-noise probes)
      • qualityMask (to exclude historically less reliable probes)
      • nonlinear dye bias correction (AKA signal quantile normalization between red/green channels across a sample)
      • calculate beta-value, m-value, or copy-number matrix
      • large batch memory management, by splitting it up into smaller batches during processing
  • 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


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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