HEARTSVG: a fast and accurate method for identifying spatially variable genes in large-scale spatial transcriptomics
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DOI: 10.1038/s41467-024-49846-1
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- Escanciano, J. Carlos & Lobato, Ignacio N., 2009. "An automatic Portmanteau test for serial correlation," Journal of Econometrics, Elsevier, vol. 151(2), pages 140-149, August.
- Moshe Sade-Feldman & Yunxin J. Jiao & Jonathan H. Chen & Michael S. Rooney & Michal Barzily-Rokni & Jean-Pierre Eliane & Stacey L. Bjorgaard & Marc R. Hammond & Hans Vitzthum & Shauna M. Blackmon & De, 2017. "Resistance to checkpoint blockade therapy through inactivation of antigen presentation," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
- Ruidong Xue & Qiming Zhang & Qi Cao & Ruirui Kong & Xiao Xiang & Hengkang Liu & Mei Feng & Fangyanni Wang & Jinghui Cheng & Zhao Li & Qimin Zhan & Mi Deng & Jiye Zhu & Zemin Zhang & Ning Zhang, 2022. "Liver tumour immune microenvironment subtypes and neutrophil heterogeneity," Nature, Nature, vol. 612(7938), pages 141-147, December.
- Lyla Atta & Jean Fan, 2021. "Computational challenges and opportunities in spatially resolved transcriptomic data analysis," Nature Communications, Nature, vol. 12(1), pages 1-5, December.
- Yi Zhang & Guanjue Xiang & Alva Yijia Jiang & Allen Lynch & Zexian Zeng & Chenfei Wang & Wubing Zhang & Jingyu Fan & Jiajinlong Kang & Shengqing Stan Gu & Changxin Wan & Boning Zhang & X. Shirley Liu , 2023. "MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment," Nature Communications, Nature, vol. 14(1), pages 1-12, 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.
- N A Heard & P Rubin-Delanchy, 2018. "Choosing between methods of combining $p$-values," Biometrika, Biometrika Trust, vol. 105(1), pages 239-246.
- John P. Sfakianos & Jorge Daza & Yang Hu & Harry Anastos & Geoffrey Bryant & Rohan Bareja & Ketan K. Badani & Matthew D. Galsky & Olivier Elemento & Bishoy M. Faltas & David J. Mulholland, 2020. "Epithelial plasticity can generate multi-lineage phenotypes in human and murine bladder cancers," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
- Ke Zhang & Wanwan Feng & Peng Wang, 2022. "Identification of spatially variable genes with graph cuts," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Kıvanç Birsoy & Richard Possemato & Franziska K. Lorbeer & Erol C. Bayraktar & Prathapan Thiru & Burcu Yucel & Tim Wang & Walter W. Chen & Clary B. Clish & David M. Sabatini, 2014. "Metabolic determinants of cancer cell sensitivity to glucose limitation and biguanides," Nature, Nature, vol. 508(7494), pages 108-112, April.
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