1 Introduction

Hello! Today we will have a closer look at two 10x Genomics Visium Gene Expression data sets generated from mouse olfactory bulb (MOB) tissue. We will go through how a general workflow can look like when processing, analyzing, and visualzing the data. The R package that we will use for this is STutility1, a tool built upon Seurat2, that is specialized at handling spatial transcriptomics (ST) and Visium data.


References:

1. Bergenstråhle J, Larsson L, Lundeberg J. Seamless integration of image and molecular analysis for spatial transcriptomics workflows. BMC Genomics. 2020 Jul 14;21(1):482. doi: 10.1186/s12864-020-06832-3. PMID: 32664861; PMCID: PMC7386244.

2. Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, Hao Y, Stoeckius M, Smibert P, Satija R. Comprehensive Integration of Single-Cell Data. Cell. 2019 Jun 13;177(7):1888-1902.e21. doi: 10.1016/j.cell.2019.05.031. Epub 2019 Jun 6. PMID: 31178118; PMCID: PMC6687398.

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