SIMS App

Overview

This app was built using Streamlit to facilitate single cell analysis in a user-friendly way. Leveraging our SIMS model, the app provides features for predicting cell types, generating explainability matrices, and performing gene pathway analysis through just three easy-to-use buttons.

If the app is live, you can access it at https://sc-sims-app.streamlit.app/.

Getting Started

To use the app, you only need a single cell dataset in the format of an .h5ad file.

Features

Predict Cell Types

• Model Selection: Choose from a list of pre-trained model checkpoints to predict cell types for your data.
• Visualization: Visualize the predicted cell types using UMAP plots.
• Download: Export the cell type predictions as a CSV file.

Generate Explainability Matrix

• Explainability Calculation: Calculate the explainability of the selected model.
• Visualization: Visualize the explainability matrix with UMAP plots.

Pathway Analysis using GSEA

• Data Upload: Upload a JSON dataset from GSEA containing a known gene pathway for comparison with your dataset.
• Gene Matching: Identify and observe which of your genes match genes from known pathways.
• Visualization: Visualize these genes and their associations using UMAP plots.

Dependencies

• scsims
• Streamlit