ArticleGenome biology2023
STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- TUSCAN: Tumor segmentation and classification analysis in spatial transcriptomics.PLoS computational biology · 2026Article
- Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications.Cancer cell · 2026Review
- Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma.Nature communications · 2025Article
- Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data.NPJ precision oncology · 2025Article
- Resolving spatial subclonal genomic heterogeneity of loss of heterozygosity and extrachromosomal DNA in gliomas.Nature communications · 2025Article
- scTML: a pan-cancer single-cell landscape of multiple mutation types.Nucleic acids research · 2025Article
- SpatialSNV: A novel method for identifying and analyzing spatially resolved SNVs in tumor microenvironments.GigaScience · 2025Article
- Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma.bioRxiv : the preprint server for biology · 2024Article
- STimage-1K4M: A histopathology image-gene expression dataset for spatial transcriptomics.Advances in neural information processing systems · 2024Article
- SIngle cell level Genotyping Using scRna Data (SIGURD).Briefings in bioinformatics · 2024Article
- STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer.Genome biology · 2023Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new software, STmut, to visualize somatic point mutations, allelic imbalance, and copy number alterations in Visium data. STmut is tested on fresh-frozen Visium data, formalin-fixed paraffin-embedded (FFPE) Visium data, and tumors with and without matching DNA sequencing data. Copy number is inferred on all conditions, but the chemistry of the FFPE platform does not permit analyses of single nucleotide variants. Taken together, we propose solutions to add the genetic dimension to spatial transcriptomic data and describe the limitations of different datatypes.
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Registered trials
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