SpaceSequest: A unified pipeline for spatial transcriptomics data analysis

Authors:

Yu (Henry) Sun¹, Sarbottam Piya¹, Zhengyu Ouyang², Yirui Chen¹, Jake Gagnon³, Shaolong Cao¹, Haotian Zhang¹, Baobao Song¹, Jing Zhu¹, Khyati Chandratre¹, Houlin Yu¹, Wenxing Hu¹, Matthew Ryals⁴, Fergal Casey¹, Dann Huh¹, Mingyao Li⁵, Baohong Zhang¹

Affiliations:

¹Research, Biogen Inc., Cambridge, MA, 02142, USA

²Data Science, BioInfoRx Inc., Madison, WI, 53719, USA

³Biostatistics, Biogen Inc., Cambridge, MA, 02142, USA

⁴PharmaLex, 1700 District Ave., Burlington, MA, 01803, USA

⁵Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA

These authors contribute equally, Yu (Henry) Sun, Sarbottam Piya, Zhengyu Ouyang

Correspondence: Yu (Henry) Sun, yuhenry.sun@biogen.com

2025-08-05

Preface

This is a user manual written using Bookdown, which provides a detailed user guide for SpaceSequest.

Cover Image: Overview of SpaceSequest components. SpaceSequest contains five modules to perform standarized data analysis generated from 10x Genomics Visium, Visium HD, and Xenium, as well as Bruker Corporation (acquired from the previous NanoString Technologies) GeoMx and CosMx platforms.