ArticleBioinformatics (Oxford, England)2022
spatialGE: quantification and visualization of the tumor microenvironment heterogeneity using spatial transcriptomics.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Article
- Spatial Transcriptomics and Dual Dye Mapping Identify Wnt-Driven BBB Protection in Endothelial EphA4-Deficiency.Research square · 2026Article
- A comparative study of statistical methods for identifying differentially expressed genes in spatial transcriptomics.PLoS computational biology · 2026Article
- Spatial Dependence and Heterogeneity in Molecular Imaging: Moran Quadrant Maps Enable Advanced Spatial-Statistical Analysis.bioRxiv : the preprint server for biology · 2025Article
- Single-cell sequencing technology in renal cancer: insights into tumor biology and clinical application.Biomarker research · 2025Review
- FUSION: a web-based application for in-depth exploration of multi-omics data with brightfield histology.Nature communications · 2025Article
- Informatics at the Frontier of Cancer Research.Cancer research · 2025Review
- Article
- STopover captures spatial colocalization and interaction in the tumor microenvironment using topological analysis in spatial transcriptomics data.Genome medicine · 2025Article
- spatialGE Is a User-Friendly Web Application That Facilitates Spatial Transcriptomics Data Analysis.Cancer research · 2025Article
- A comparative study of statistical methods for identifying differentially expressed genes in spatial transcriptomics.bioRxiv : the preprint server for biology · 2025Article
- Article
- Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment.Genome biology · 2024Article
- SpottedPy quantifies relationships between spatial transcriptomic hotspots and uncovers environmental cues of epithelial-mesenchymal plasticity in breast cancer.Genome biology · 2024Article
- spatialGE: A user-friendly web application to democratize spatial transcriptomics analysis.bioRxiv : the preprint server for biology · 2024Article
- Spatial transcriptomics analysis identifies a tumor-promoting function of the meningeal stroma in melanoma leptomeningeal disease.Cell reports. Medicine · 2024Article
- Differential gene expression analysis of spatial transcriptomic experiments using spatial mixed models.Scientific reports · 2024Article
- SRT-Server: powering the analysis of spatial transcriptomic data.Genome medicine · 2024Article
- Spatial transcriptomics analysis identifies a unique tumor-promoting function of the meningeal stroma in melanoma leptomeningeal disease.bioRxiv : the preprint server for biology · 2023Article
- Systems immunology spanning tumors, lymph nodes, and periphery.Cell reports methods · 2023Review
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Authors and funding
7 authors.
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Abstract
summarySpatially resolved transcriptomics promises to increase our understanding of the tumor microenvironment and improve cancer prognosis and therapies. Nonetheless, analytical methods to explore associations between the spatial heterogeneity of the tumor and clinical data are not available. Hence, we have developed spatialGE, a software that provides visualizations and quantification of the tumor microenvironment heterogeneity through gene expression surfaces, spatial heterogeneity statistics that can be compared against clinical information, spot-level cell deconvolution and spatially informed clustering, all using a new data object to store data and resulting analyses simultaneously. AVAILABILITY AND IMPLEMENTATION: The R package and tutorial/vignette are available at https://github.com/FridleyLab/spatialGE. A script to reproduce the analyses in this manuscript is available in Supplementary information. The Thrane study data included in spatialGE was made available from the public available from the website https://www.spatialresearch.org/resources-published-datasets/doi-10-1158-0008-5472-can-18-0747/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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