methylcheck
is a Python-based package for filtering and visualizing Illumina methylation array data. The focus is on quality control. View on ReadTheDocs.
methylcheck
is part of the methylsuite of python packages that provide functions to process and analyze DNA methylation data from Illumina's Infinium arrays (27k, 450k, and EPIC, as well as mouse arrays). This package is focused on quality control for processed methylation data.
methylcheck
functions are designed to work with a minimum of knowledge and specification required. But you can always override the "smart" defaults with custom settings if the default settings don't work for your data. The entire methylsuite
is designed in this format: to offer ease of use while still maintaining flexibility for customization as needed.
You should install all three components, as they work together. The parts include:
methylprep
: for processing idat
files or downloading GEO datasets from NIH. Processing steps include
methylcheck
: (this package) for quality control (QC) and analysis, including
methylprep process
will exclude a set of unreliable probes by default. You can disable that using the --no_quality_mask option from CLI.seaborn
and matplotlib
graphic libraries.methylize
provides more analysis and interpretation functions
methylcheck
maintains configuration files for your Python package manager of choice: pipenv or pip. Conda install is coming soon.
>>> pip install methylcheck
or if you want to install all three packages at once (recommended):
>>> pip install methylsuite
If you are new to DNA methylation analysis, we recommend reading through this introduction from the methylprep
documentation. Otherwise, you are ready to use methylcheck
to: