SpatialOne: end-to-end analysis of visium data at scale.

ABSTRACT:

Motivation

Spatial transcriptomics allow to quantify mRNA expression within the spatial context. Nonetheless, in-depth analysis of spatial transcriptomics data remains challenging and difficult to scale due to the number of methods and libraries required for that purpose.

Results

Here we present SpatialOne, an end-to-end pipeline designed to simplify the analysis of 10x Visium data by combining multiple state-of-the-art computational methods to segment, deconvolve, and quantify spatial information; this approach streamlines the analysis of reproducible spatial-data at scale.

Availability and implementation

SpatialOne source code and execution examples are available at https://github.com/Sanofi-Public/spatialone-pipeline, experimental data is available at https://zenod

SUBMITTER: Kamel M 

PROVIDER: S-EPMC11374018 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature