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---
title: "Home"
site: workflowr::wflow_site
output:
workflowr::wflow_html:
toc: false
---
# Gene set testing for methylation arrays
This site contains the development and evaluation of various methylation array
gene set testing methods available in the Bioconductor [missMethyl package](https://bioconductor.org/packages/release/bioc/html/missMethyl.html).
Follow the links below to explore the
different parts of the project.
Analysis
--------
* Explore EPIC array bias
* [EPIC array bias](exploreArrayBiasEPIC.html) - Explore the various
array biases that affect gene set testing.
* Explore 450k array bias
* [450k array bias](exploreArrayBias450.html) - Explore the various
array biases that affect gene set testing.
* Compare methods
* [Compare methods](exploreData.html) - Analyse an EPIC array sorted blood cell
dataset using various gene set testing methods. Compare the results of the different
methods.
* Compare false discovery rate of different methods
* [Compare false discovery rate](fdrAnalysis.html) - Analyse the normal samples from
a 450k array KIRC TCGA dataset using various genset testing methods to
estimate their false discovery rate control.
* Gene set testing of regions
* [Region analysis](regionAnalysis.html) - Evalulate the use of gometh for geneset
testing of differentially methylated regions from region finding software.
Licenses
--------
The code in this analysis is covered by the [MIT license][mit] and the written
content on this website is covered by a [Creative Commons CC-BY][cc] license.
Citations
---------
[mit]: https://choosealicense.com/licenses/mit/ "MIT License"
[cc]: https://creativecommons.org/licenses/by/4.0/ "CC-BY License"