---
title: Cases study
bibliography: bibliography.bib
date: "`r BiocStyle::doc_date()`"
vignette: >
  %\VignetteIndexEntry{"5. Cases study"}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---


# Case: Integration of DNA methylation and gene expression for TCGA adrenal cortical carcinoma (ACC) samples

In this case study, we downloaded DNA methylation and gene expression for TCGA adrenal cortical carcinoma (ACC) samples, executed the Differentially methylated region (DMR) analysis and Differential Expression Analysis  (DEA),  then both results were integrated into a starburst plot.

<center>
[![IMAGE ALT TEXT](http://img.youtube.com/vi/RcXibjFanH4/maxresdefault.jpg)](http://www.youtube.com/watch?v=RcXibjFanH4 "Tutorial video: Integration of methylation and expression for TCGA adrenal cortical carcinoma (ACC) samples - (http://www.youtube.com/watch?v=RcXibjFanH4)")

<center>**Tutorial Video:** Integration of methylation and expression for TCGA adrenal cortical carcinoma (ACC) samples - (http://www.youtube.com/watch?v=RcXibjFanH4)
</center>

# Case: Executing ELMER analysis on TCGA Kidney renal clear cell carcinoma (KIRC) samples

In this case, we downloaded DNA methylation and gene expression data for TCGA Kidney renal clear cell carcinoma (KIRC) samples. Then, this data is used to execute [ELMER](http://bioconductor.org/packages/ELMER/) analysis. 

For a more detailed example, please check our [Bioc2017 workshop](https://bioinformaticsfmrp.github.io/Bioc2017.TCGAbiolinks.ELMER/index.html).


<center>
[![IMAGE ALT TEXT](http://img.youtube.com/vi/EhGw1aF-2_c/maxresdefault.jpg)](http://www.youtube.com/watch?v=EhGw1aF-2_c "Tutorial video: Executing Elmer analysis on TCGA Kidney renal clear cell carcinoma (KIRC) samples - (http://www.youtube.com/watch?v=EhGw1aF-2_c)")

**Tutorial Video:** Executing Elmer analysis on TCGA Kidney renal clear cell carcinoma (KIRC) samples - (http://www.youtube.com/watch?v=EhGw1aF-2_c)
</center>