Software

Searching and visualizing genetic associations of pregnancy traits

• Website: https://gnumom2b.cumcobgyn.org/
• Yan, Q., Guerrero, R.F., Khan, R.R., Surujnarine, A.A., Wapner, R.J., et al. (2023). Searching and visualizing genetic associations of pregnancy traits by using GnuMoM2b. Genetics.

Late AMD Fundus Image Prediction

• 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 Intelligence.

Computer-Aided Risk Estimation for AMD in Caucasians

• Website: https://yanq.shinyapps.io/no_vs_amd_NN/
• Yan, Q., Jiang, Y., Huang, H., Swaroop, A., Chew, E.Y., Weeks, D.E., Chen, W., and Ding, Y. (2020). GWAS-based Machine Learning for Prediction of Age-Related Macular Degeneration Risk. TVST.

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.

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.

CHIT

Combined Haplotype Interaction Test (CHIT)

• Source code: https://github.com/QiYanPitt/CHIT
• Yan, Q., Forno, E., Celedon, J.C., Chen. W., Weeks, D.E. (2021). Allele-specific method for testing the association between molecular quantitative traits and phenotype-genotype interaction. Bioinformatics.

MRmediation

Causal Mediation Method with Methylated Region (MR) as the Mediator

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