Python-based Illumina methylation array processing and analysis software composite package
This meta package will install the python packages that together make up the
methylprepis 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
- 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.
methylizeprovides 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).
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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