Topological identification and interpretation for single-cell gene regulation elucidation across multiple platforms using scMGCA
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DOI: 10.1038/s41467-023-36134-7
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- 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.
- Xiangjie Li & Kui Wang & Yafei Lyu & Huize Pan & Jingxiao Zhang & Dwight Stambolian & Katalin Susztak & Muredach P. Reilly & Gang Hu & Mingyao Li, 2020. "Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
- Sara Mostafavi & Anna Goldenberg & Quaid Morris, 2012. "Labeling Nodes Using Three Degrees of Propagation," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-10, December.
- William Stephenson & Laura T. Donlin & Andrew Butler & Cristina Rozo & Bernadette Bracken & Ali Rashidfarrokhi & Susan M. Goodman & Lionel B. Ivashkiv & Vivian P. Bykerk & Dana E. Orange & Robert B. D, 2018. "Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
- Duc Tran & Hung Nguyen & Bang Tran & Carlo La Vecchia & Hung N. Luu & Tin Nguyen, 2021. "Fast and precise single-cell data analysis using a hierarchical autoencoder," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
- Gökcen Eraslan & Lukas M. Simon & Maria Mircea & Nikola S. Mueller & Fabian J. Theis, 2019. "Single-cell RNA-seq denoising using a deep count autoencoder," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
- 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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