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EpiMix

An intergrative tool for epigenomic subtyping using DNA methylation


### Introduction EpiMix is a comprehensive tool for the integrative analysis of DNA methylation data and gene expression data (**Figure 1**). EpiMix enables automated data downloading (from TCGA or GEO), pre-processing, methylation modeling, interactive visualization and functional annotation. To identify hypo- or hypermethylated genes, EpiMix uses a beta mixture model to identify the methylation states of each CpG site and compares the DNA methylation in an experimental group to a control group. The output from EpiMix is the functional changes in DNA methylation that is associated with gene expression.

EpiMix incorporates specialized algorithms to identify functional DNA methylation at various genetic elements, including proximal cis-regulatory elements of protein-coding genes, distal enhancers, and genes encoding microRNAs (miRNAs) or lncRNAs. There are four alternative analytic modes for modeling DNA methylation at different genetic elements:

  • Regular: cis-regulatory elements within or immediately surrounding protein-coding genes.
  • Enhancer: distal enhancers.
  • miRNA: miRNA-coding genes.
  • lncRNA: lncRNA-coding genes.

Figure 1. Overview of EpiMix's workflow. EpiMix incorporates four functional modules: downloading, preprocessing, methylation modeling and functional analysis. The methylation modeling module enables four alternative analytic modes, including "Regular", "Enhancer", "miRNA" and "lncRNA". These analytic modes target DNA methylation analysis on different genetic elements.


Interactive web tool

EpiMix is also available as an interactive web tool: https://epimix.stanford.edu


Authors


Yuanning Zheng, John Jun, Kevin Brennan and Olivier Gevaert
Stanford Center for Biomedical Informatics Research (BIMR)
Department of Medicine
1265 Welch Road
Stanford CA, 94305-5479


epimix's People

Contributors

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Stargazers

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Watchers

James Cloos avatar Pritam Mukherjee avatar

epimix's Issues

Prepare for upcoming Seurat v5 release

I am opening this issue as a notification because EpiMix is listed here as a package that relies (depends/imports/suggests) on Seurat. As you may know, we recently released Seurat v5 as a beta in March of this year, with new updates for spatial, multimodal, and massively scalable analysis. For more information on updates and improvements, check out our website https://satijalab.org/seurat/.
We are now preparing to release Seurat v5 to CRAN, and plan to submit it on October 23rd. While we have tried our best to keep things backward-compatible, it is possible that updates to Seurat and SeuratObject might break your existing functionality or tests. We wanted to reach out before the new version is on CRAN, so that there's time to report issues/incompatibilities and prepare you for any changes in your code base that might be necessary.

We apologize for any disruption or inconvenience, but hope that the improvements to Seurat v5 will benefit your users going forward.
To test the upcoming release, you can install Seurat from the seurat5 branch using the instructions available on this page: https://satijalab.org/seurat/articles/install.

Thank you!
Seurat v5 team

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