# PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns

## TL;DR

PreTSA is a fast and efficient method for analyzing gene expression patterns in large single-cell and spatial transcriptomics datasets.

## Contribution

PreTSA introduces a computationally efficient approach that matches state-of-the-art results while reducing processing time for large datasets.

## Key findings

- PreTSA matches state-of-the-art methods in modeling gene expression patterns.
- It significantly reduces computational time for large-scale datasets.
- PreTSA is applicable to both single-cell and spatial transcriptomics data.

## Abstract

Modeling temporal and spatial gene expression patterns in large-scale single-cell and spatial transcriptomics data is a computationally intensive task. We present PreTSA, a method that offers computational efficiency in modeling these patterns and is applicable to single-cell and spatial transcriptomics data comprising millions of cells. PreTSA consistently matches the results of state-of-the-art methods while significantly reducing computational time. PreTSA provides a unique solution for studying gene expression patterns in extremely large datasets.

The online version contains supplementary material available at 10.1186/s13059-026-03994-3.