Methodology research

Mediation

• Source code: https://cran.r-project.org/web/packages/MRmediation/index.html
• Yan, Q., Forno, E., Celedon, J.C., and Chen, W. (2021). A region-based method for causal mediation analysis of DNA methylation data. Epigenetics in press.

Deep Learning

• Website: http://54.242.15.216/calculator/
• Source code: https://github.com/QiYanPitt/AMDprogressCNN
• Yan, Q., Weeks, D.E., Xin, H., Swaroop, A., Chew, E.Y., Huang, H., Ding, Y., and Chen, W. (2020). Deep-learning-based Prediction of Late Age-Related Macular Degeneration Progression Nature Machine Intellegence 2, 141-150.

Multi-Omics Data

• Source code: https://cran.r-project.org/web/packages/OmnibusFisher/index.html
• Yan, Q., Liu, N., Forno, E., Canino, G., Celedon, J.C., and Chen, W. (2019). An integrative association method for omics data based on a modified Fisher’s method with application to childhood asthma. PLoS Genet 15, e1008142.
  
  

Allelic Imbalance

• Source code: https://github.com/QiYanPitt/CHIT

Methods for Genetic Association Tests

KMgene: A unified R package for gene-based association analysis for complex traits

• Source code: https://cran.r-project.org/web/packages/KMgene/index.html
• Yan, Q., Fang, Z., and Chen, W. (2018). KMgene: a unified R package for gene-based association analysis for complex traits. Bioinformatics 34, 2144-2146.