MIAMI-AD (Methylation in Aging and Methylation in AD): an integrative knowledgebase that facilitates explorations of DNA methylation across sex, aging, and Alzheimer’s disease
David Lukacsovich, Deirdre O’Shea, Hanchen Huang, Wei Zhang, Juan Young, X. Steven Chen, Sven-Thorsten Dietrich, Brian Kunkle, Eden Martin, Lily Wang
Lukacsovich D et al. (2024) MIAMI-AD (Methylation in Aging and Methylation in AD): an integrative knowledgebase that facilitates explorations of DNA methylation across sex, aging, and Alzheimer's disease. Oxford Academic
Please also cite the original study papers in which the results were obtained.
We created MIAMI-AD, a comprehensive knowledge base containing manually curated summary statistics from recent studies, all of which included at least 100 participants. MIAMI-AD enables easy browsing, querying, and downloading DNAm associations at multiple levels – at individual CpG, gene, genomic regions, or genome-wide, in one or multiple studies. Moreover, it also offers tools to perform integrative analyses, such as comparing DNAm associations across different phenotypes or tissues, as well as interactive visualizations. This open-access resource is freely available to the research community, and all the underlying data can be downloaded. MIAMI-AD (https://miami-ad.org) facilitates integrative explorations to better understand the interplay between DNAm across aging, sex, and AD.
If you wish to run MIAMI-AD on your own computer, the code can be downloaded and installed using
library(devtools)
install_github("TransBioInfoLab/MIAMI.AD")
This repository is missing the SQLite database file (3.2 GB) that contains the detabase information. It's hosted on Box. To run MIAMI-AD on your own server, it needs to be downloaded and placed in the inst/shiny/Data/SQL_DBs directory.
Once installed, it can be run via
MIAMI.AD::run_app()
Or running the app.r file in the main directory.
For instructions on using the database, click on the Tutorial tab. Alternatively, in each tab there is a Start Tutorial button at the top left, which gives a brief overview of the relevant tab.