MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer
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DOI: 10.1038/s41467-023-44570-8
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- Aashi Jindal & Prashant Gupta & Jayadeva & Debarka Sengupta, 2018. "Discovery of rare cells from voluminous single cell expression data," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
- Anjun Ma & Xiaoying Wang & Jingxian Li & Cankun Wang & Tong Xiao & Yuntao Liu & Hao Cheng & Juexin Wang & Yang Li & Yuzhou Chang & Jinpu Li & Duolin Wang & Yuexu Jiang & Li Su & Gang Xin & Shaopeng Gu, 2023. "Single-cell biological network inference using a heterogeneous graph transformer," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Katharina T. Schmid & Barbara Höllbacher & Cristiana Cruceanu & Anika Böttcher & Heiko Lickert & Elisabeth B. Binder & Fabian J. Theis & Matthias Heinig, 2021. "scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
- Juexin Wang & Anjun Ma & Yuzhou Chang & Jianting Gong & Yuexu Jiang & Ren Qi & Cankun Wang & Hongjun Fu & Qin Ma & Dong Xu, 2021. "scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
- Botao Fa & Ting Wei & Yuan Zhou & Luke Johnston & Xin Yuan & Yanran Ma & Yue Zhang & Zhangsheng Yu, 2021. "GapClust is a light-weight approach distinguishing rare cells from voluminous single cell expression profiles," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
- Kenji Kamimoto & Blerta Stringa & Christy M. Hoffmann & Kunal Jindal & Lilianna Solnica-Krezel & Samantha A. Morris, 2023. "Dissecting cell identity via network inference and in silico gene perturbation," Nature, Nature, vol. 614(7949), pages 742-751, February.
- Eirini Arvaniti & Manfred Claassen, 2017. "Sensitive detection of rare disease-associated cell subsets via representation learning," Nature Communications, Nature, vol. 8(1), pages 1-10, April.
- Suoqin Jin & Christian F. Guerrero-Juarez & Lihua Zhang & Ivan Chang & Raul Ramos & Chen-Hsiang Kuan & Peggy Myung & Maksim V. Plikus & Qing Nie, 2021. "Inference and analysis of cell-cell communication using CellChat," Nature Communications, Nature, vol. 12(1), pages 1-20, December.
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- Yunpei Xu & Shaokai Wang & Qilong Feng & Jiazhi Xia & Yaohang Li & Hong-Dong Li & Jianxin Wang, 2024. "scCAD: Cluster decomposition-based anomaly detection for rare cell identification in single-cell expression data," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
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