memeth

A Snakemake workflow to analyse Illumina methylation arrays

Contents

• Overview
• Installation
• Usage
• Documentation
• Contributing
• Authors
• Citation
• Acknowledgements
• License

Overview

This workflow is used to analyse Illumina methylation arrays at the probe level. It performs quality control, filtering, normalization, data exploration and differential methylation testing.

Installation

Install Snakemake using the conda package manager:

$ conda create -c bioconda -c conda-forge --name snakemake snakemake

Deploy the workflow to your project directory:

$ git pull https://github.com/zifornd/arrays projects/arrays

Usage

Configure the workflow by editing the config.yaml file:

$ nano config/config.yaml

Define the samples by editing the samples.tsv file:

$ nano config/samples.tsv

Execute the workflow and install dependencies:

$ snakemake --cores all --use-conda 

Documentation

See the Documentation file for all configuration, execution, and output information.

Contributing

See the Contributing file for ways to get started.

Please adhere to this project's Code of Conduct.

Authors

This workflow was developed by:

• Benjamin Southgate
• James Ashmore

Citation

See the Citation file for ways to cite this workflow.

Acknowledgements

This workflow is based on the following research article:

Maksimovic J, Phipson B and Oshlack A. A cross-package Bioconductor workflow for analysing methylation array data [version 3; peer review: 4 approved]. F1000Research 2017, 5:1281 (https://doi.org/10.12688/f1000research.8839.3)

License

This workflow is licensed under the MIT license.
Copyright © 2021, Zifo RnD Solutions