SONAR enables cell type deconvolution with spatially weighted Poisson-Gamma model for spatial transcriptomics
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DOI: 10.1038/s41467-023-40458-9
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- Bosiljka Tasic & Zizhen Yao & Lucas T. Graybuck & Kimberly A. Smith & Thuc Nghi Nguyen & Darren Bertagnolli & Jeff Goldy & Emma Garren & Michael N. Economo & Sarada Viswanathan & Osnat Penn & Trygve B, 2018. "Shared and distinct transcriptomic cell types across neocortical areas," Nature, Nature, vol. 563(7729), pages 72-78, November.
- Mor Nitzan & Nikos Karaiskos & Nir Friedman & Nikolaus Rajewsky, 2019. "Gene expression cartography," Nature, Nature, vol. 576(7785), pages 132-137, December.
- Xuran Wang & Jihwan Park & Katalin Susztak & Nancy R. Zhang & Mingyao Li, 2019. "Bulk tissue cell type deconvolution with multi-subject single-cell expression reference," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
- Anjali Rao & Dalia Barkley & Gustavo S. França & Itai Yanai, 2021. "Exploring tissue architecture using spatial transcriptomics," Nature, Nature, vol. 596(7871), pages 211-220, August.
- Kangning Dong & Shihua Zhang, 2022. "Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Meng Zhang & Stephen W. Eichhorn & Brian Zingg & Zizhen Yao & Kaelan Cotter & Hongkui Zeng & Hongwei Dong & Xiaowei Zhuang, 2021. "Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH," Nature, Nature, vol. 598(7879), pages 137-143, October.
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