StPipe: a flexible and streamlined R/Bioconductor pipeline for preprocessing sequencing-based spatial transcriptomics data.

ABSTRACT: Spatial transcriptomics technology has developed rapidly in recent years, with various sequencing-based platforms such as 10× Visium, Slide-seq, and Stereo-seq becoming widely used by researchers. Each platform brings its own set of protocols and customized data analysis pipelines, which presents challenges when the goal is to obtain uniformly preprocessed data that is conveniently formatted for downstream analysis. To address the need for simpler, open-source solutions that deal with sequencing-based spatial transcriptomics (sST) data from different platforms, we present stPipe, a comprehensive and modular preprocessing pipeline for all current mainstream sST platforms. stPipe is implemented as an R/Bioconductor package that handles various analysis steps, including (i) data processing fr

SUBMITTER: Xu Y 

PROVIDER: S-EPMC12639247 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature