Resources

Spatial Aging Clocks Spatial aging clocks for cell types in the mouse brain

Tools for deploying our spatial aging clock models (trained on mouse brain data) to a single-cell datasets (both spatial or non-spatial).

Spatial Aging Datasets MERFISH Datasets for Mouse Brain Aging, Exercise & Reprogramming

This Zenodo repository contains AnnData objects containing the processed MERFISH spatial transcriptomics datasets for mouse brain aging, experiments with exercise, and experiments with partial reprogramming.

TISSUE Uncertainty-aware spatial gene expression prediction

TISSUE (Transcript Imputation with Spatial Single-cell Uncertainty Estimation) provides tools for estimating well-calibrated uncertainty measures for gene expression predictions in single-cell spatial transcriptomics datasets and utilizing them in downstream analyses.

SPRITE Cell and gene networks for spatial gene expression prediction

SPRITE (Spatial Propagation and Reinforcement of Imputed Transcript Expression) is a meta-algorithm for post-processing spatial gene expression predictions to improve the quality of predictions and their utility in downstream analysis.

DynamicViz Dynamic visualization of high-dimensional data

DynamicViz package for generating bootstrap visualizations of high-dimensional data. Great for assessing stability of visualizations and increasing robustness of interpretations.