HiyanZhang / Roche-PMDA-Summer-School

Roche PMDA (Predictive Modeling and Data Analytics) Summer School 2023-Computational toxicology

Roche PMDA (Predictive Modeling and Data Analytics) Summer School 2023-Computational toxicology

Data set

the data used in this summer school are from the publication by Manuela Jaklin et al.. “Optimization of the TeraTox Assay for Preclinical Teratogenicity Assessment.” Toxicological Sciences 188, no. 1 (July 1, 2022): 17–33. https://doi.org/10.1093/toxsci/kfac046. Explore the supplementary differential gene expression data of the TeraTox assay, available at https://zenodo.org/record/6143691.

Data exploration

In this section, we visualized the gene count data and logFC data using PCA and UMAP

Machine-learning models

In this section, we have built different machine-learning models to predict teratogenicity potentials based on gene expression data as input.

References

Jaklin, Manuela, et al. "Optimization of the TeraTox assay for preclinical teratogenicity assessment." Toxicological Sciences 188.1 (2022): 17-33.