SpaceSequest: pipeline for spatial transcriptomics data analysis

Yu (Henry) Sun (Corresponding Author)

Biogen
yuhenry.sun@biogen.com

Sarbottam Piya

Biogen

Zhengyu Ouyang

BioInfoRx

Jake Gagnon

Biogen

Yirui Chen

Biogen

Shaolong Cao

Biogen

Haotian Zhang

Biogen

Baobao Song

Biogen

Jing Zhu

Biogen

Khyati Chandratre

Biogen

Houlin Yu

Biogen

Wenxing Hu

Biogen

Matthew Ryals

PharmaLex

Fergal Cassey

Biogen

Dann Huh

Biogen

Mingyao Li

University of Pennsylvania

Baohong Zhang

Biogen

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

2025-06-25

Chapter 1 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 (acquired from the previous NanoString Technologies) GeoMx and CosMx platforms.