More details
This app provides a comprehensive platform for exploring gene expression and SHAP (SHapley Additive exPlanations) features in preimplantation mouse and human development. Users can analyze differentially expressed genes (DEGs) across cell types and developmental stages, as well as examine SHAP features to understand the impact of individual genes on model predictions.
For the analysis of differentially expressed genes, users can select the species (human or mouse) and the dataset type (cell type or stage) from a sidebar menu. The app offers options to filter DEGs based on criteria such as log2 fold-change and adjusted p-value, allowing researchers to focus on genes of interest. The resulting subset of DEGs is displayed in a dataframe, facilitating further exploration and analysis.
Additionally, users can explore SHAP features by selecting the dataset (human or mouse) from the sidebar. They can then choose a specific cell type and select genes of interest to examine the SHAP values associated with those genes. The app provides an interactive dataframe displaying the SHAP features, enabling users to identify genes that contribute significantly to model predictions across different cell types.
Overall, this app offers a user-friendly interface for investigating gene expression patterns and understanding the contributions of individual genes to preimplantation development in both mouse and human embryos.
See owner's GitHub repository for more information: https://github.com/brickmanlab/preimplantation-portal.
This app is based on the paper:
Proks, M., Salehin, N., & Brickman, J. M. (2024). Deep Learning Based Models for Preimplantation Mouse and Human Development. bioRxiv, 2024.02.16.580649. https://doi.org/10.1101/2024.02.16.580649
AI models:
Trained models with parameters were uploaded to Hugging Face: https://huggingface.co/brickmanlab/preimplantation-models
Models: scANVI, scANVI [ns=15], XGBoost, scVI, scANVI, scGEN
This application was not uploaded by the author, but through their publicly available Github repository, https://github.com/brickmanlab/preimplantation-portal.
Warning: Not intended for clinical use. Assume outputs are unsafe and unvalidated. Use carefully.
- Precision Medicine & Genomics