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PreTSA

The R package PreTSA (Pattern recognition in Temporal and Spatial Analyses) performs computationally efficient modeling of temporal and spatial gene expression patterns in large-scale single-cell and spatial transcriptomics data, providing a unique solution for understanding dynamic biological processes.

Installation

To install the latest version of the R package from GitHub, please run following commands in R:

if (!require("devtools"))
install.packages("devtools")
devtools::install_github("haotian-zhuang/PreTSA")

For users with suitable hardware and technical expertise, non-standard R installations may further increase the computational efficiency of PreTSA. For example, using a threaded MKL-based R installation, such as one installed via a package manager like conda, may reduce computation time by more efficiently parallelizing matrix operations.

Vignettes

Detailed vignettes are available at this website.

Vignette: Model temporal gene expression patterns

Vignette: Model spatial gene expression patterns

Citation

Please cite the following paper: Haotian Zhuang and Zhicheng Ji. PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns. Genome Biology (2026).

Contact

Authors: Haotian Zhuang, Zhicheng Ji

Report bugs and provide suggestions by sending email to:

Maintainer: Haotian Zhuang ()

Or open a new issue on this GitHub page