STANCE: a unified statistical model to detect cell-type-specific spatially variable genes in spatial transcriptomics
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-025-57117-w
Download full text from publisher
References listed on IDEAS
- Lulu Shang & Xiang Zhou, 2022. "Spatially aware dimension reduction for spatial transcriptomics," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
- Brendan F. Miller & Feiyang Huang & Lyla Atta & Arpan Sahoo & Jean Fan, 2022. "Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
- Dawei Liu & Xihong Lin & Debashis Ghosh, 2007. "Semiparametric Regression of Multidimensional Genetic Pathway Data: Least-Squares Kernel Machines and Linear Mixed Models," Biometrics, The International Biometric Society, vol. 63(4), pages 1079-1088, December.
- Guanao Yan & Shuo Harper Hua & Jingyi Jessica Li, 2025. "Categorization of 34 computational methods to detect spatially variable genes from spatially resolved transcriptomics data," Nature Communications, Nature, vol. 16(1), pages 1-21, December.
- Lawrence Hubert & Phipps Arabie, 1985. "Comparing partitions," Journal of Classification, Springer;The Classification Society, vol. 2(1), pages 193-218, December.
- Alma Andersson & Ludvig Larsson & Linnea Stenbeck & Fredrik Salmén & Anna Ehinger & Sunny Z. Wu & Ghamdan Al-Eryani & Daniel Roden & Alex Swarbrick & Åke Borg & Jonas Frisén & Camilla Engblom & Joakim, 2021. "Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
- Lukas M. Weber & Arkajyoti Saha & Abhirup Datta & Kasper D. Hansen & Stephanie C. Hicks, 2023. "nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Yanming Ren & Zongyao Huang & Lingling Zhou & Peng Xiao & Junwei Song & Ping He & Chuanxing Xie & Ran Zhou & Menghan Li & Xiangqun Dong & Qing Mao & Chao You & Jianguo Xu & Yanhui Liu & Zhigang Lan & , 2023. "Spatial transcriptomics reveals niche-specific enrichment and vulnerabilities of radial glial stem-like cells in malignant gliomas," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
- Lulu Shang & Xiang Zhou, 2022. "Spatially aware dimension reduction for spatial transcriptomics," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
- Wu, Han-Ming & Tien, Yin-Jing & Chen, Chun-houh, 2010. "GAP: A graphical environment for matrix visualization and cluster analysis," Computational Statistics & Data Analysis, Elsevier, vol. 54(3), pages 767-778, March.
- José E. Chacón, 2021. "Explicit Agreement Extremes for a 2 × 2 Table with Given Marginals," Journal of Classification, Springer;The Classification Society, vol. 38(2), pages 257-263, July.
- Roberto Rocci & Stefano Antonio Gattone & Roberto Di Mari, 2018. "A data driven equivariant approach to constrained Gaussian mixture modeling," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 12(2), pages 235-260, June.
- Redivo, Edoardo & Nguyen, Hien D. & Gupta, Mayetri, 2020. "Bayesian clustering of skewed and multimodal data using geometric skewed normal distributions," Computational Statistics & Data Analysis, Elsevier, vol. 152(C).
- Zhu, Xuwen & Melnykov, Volodymyr, 2018. "Manly transformation in finite mixture modeling," Computational Statistics & Data Analysis, Elsevier, vol. 121(C), pages 190-208.
- Amiri, Babak & Karimianghadim, Ramin, 2024. "A novel text clustering model based on topic modelling and social network analysis," Chaos, Solitons & Fractals, Elsevier, vol. 181(C).
- Li, Pai-Ling & Chiou, Jeng-Min, 2011. "Identifying cluster number for subspace projected functional data clustering," Computational Statistics & Data Analysis, Elsevier, vol. 55(6), pages 2090-2103, June.
- A van Giessen & K G M Moons & G A de Wit & W M M Verschuren & J M A Boer & H Koffijberg, 2015. "Tailoring the Implementation of New Biomarkers Based on Their Added Predictive Value in Subgroups of Individuals," PLOS ONE, Public Library of Science, vol. 10(1), pages 1-14, January.
- Yaeji Lim & Hee-Seok Oh & Ying Kuen Cheung, 2019. "Multiscale Clustering for Functional Data," Journal of Classification, Springer;The Classification Society, vol. 36(2), pages 368-391, July.
- Zaili Fang & Inyoung Kim & Jeesun Jung, 2018. "Semiparametric Kernel-Based Regression for Evaluating Interaction Between Pathway Effect and Covariate," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 23(1), pages 129-152, March.
- Stefano Tonellato & Andrea Pastore, 2013. "On the comparison of model-based clustering solutions," Working Papers 2013:05, Department of Economics, University of Venice "Ca' Foscari".
- Elvira Pelle & Roberta Pappadà, 2021. "A clustering procedure for mixed-type data to explore ego network typologies: an application to elderly people living alone in Italy," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 30(5), pages 1507-1533, December.
- Renato Cordeiro Amorim, 2016. "A Survey on Feature Weighting Based K-Means Algorithms," Journal of Classification, Springer;The Classification Society, vol. 33(2), pages 210-242, July.
- Tom Wilderjans & Eva Ceulemans & Iven Mechelen, 2008. "The CHIC Model: A Global Model for Coupled Binary Data," Psychometrika, Springer;The Psychometric Society, vol. 73(4), pages 729-751, December.
- Dong Liu & Changwei Zhao & Yong He & Lei Liu & Ying Guo & Xinsheng Zhang, 2023. "Simultaneous cluster structure learning and estimation of heterogeneous graphs for matrix‐variate fMRI data," Biometrics, The International Biometric Society, vol. 79(3), pages 2246-2259, September.
- Yuchen Liang & Guowei Shi & Runlin Cai & Yuchen Yuan & Ziying Xie & Long Yu & Yingjian Huang & Qian Shi & Lizhe Wang & Jun Li & Zhonghui Tang, 2024. "PROST: quantitative identification of spatially variable genes and domain detection in spatial transcriptomics," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Jeffrey Andrews & Paul McNicholas, 2014. "Variable Selection for Clustering and Classification," Journal of Classification, Springer;The Classification Society, vol. 31(2), pages 136-153, July.
- Marek Obrębalski & Marek Walesiak, 2015. "Functional structure of Polish regions in the period 2004-2013 – measurement via HHI Index, Florence’s coefficient of localization and cluster analysis," Statistics in Transition new series, Główny Urząd Statystyczny (Polska), vol. 16(2), pages 223-242, June.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-57117-w. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.