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A Gentle Introduction to Spatial Transcriptomic Analysis with 10X Visium Data

Gillespie, J.; Xie, J.; Jung, K. J.; Hardiman, G.; Pietrzak, M.; Chung, D.

2025-05-07 bioinformatics
10.1101/2025.05.01.651786 bioRxiv
Show abstract

Spatial transcriptomics (ST) combines single-cell RNA-seq gene expression data with spatial coordinates to provide an accurate, 2D picture of gene expression across a tissue sample. With this technology, we can discover detailed RNA localization, study development, investigate the tumor microenvironment, and create a tissue atlas. Full ST analysis requires several steps, however, as this protocol aims to be a simple introduction to the analysis process, only the foundational steps of clustering, spatially variable gene discovery, and cell-cell communication are presented, focusing on data obtained from the 10X Genomics Visium platform. An expanded protocol with full code is available at https://github.com/j-gillespie-dna/STanalysis.git

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.