scLENS: data-driven signal detection for unbiased scRNA-seq data analysis
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DOI: 10.1038/s41467-024-47884-3
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- Peng Qiu, 2020. "Embracing the dropouts in single-cell RNA-seq analysis," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
- John Horn, 1965. "A rationale and test for the number of factors in factor analysis," Psychometrika, Springer;The Psychometric Society, vol. 30(2), pages 179-185, June.
- Jong Kyoung Kim & Aleksandra A. Kolodziejczyk & Tomislav Ilicic & Sarah A. Teichmann & John C. Marioni, 2015. "Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression," Nature Communications, Nature, vol. 6(1), pages 1-9, December.
- Koen Van den Berge & Hector Roux de Bézieux & Kelly Street & Wouter Saelens & Robrecht Cannoodt & Yvan Saeys & Sandrine Dudoit & Lieven Clement, 2020. "Trajectory-based differential expression analysis for single-cell sequencing data," Nature Communications, Nature, vol. 11(1), pages 1-13, 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.
- Roshan M. Kumar & Patrick Cahan & Alex K. Shalek & Rahul Satija & A. Jay DaleyKeyser & Hu Li & Jin Zhang & Keith Pardee & David Gennert & John J. Trombetta & Thomas C. Ferrante & Aviv Regev & George Q, 2014. "Deconstructing transcriptional heterogeneity in pluripotent stem cells," Nature, Nature, vol. 516(7529), pages 56-61, December.
- George C. Linderman & Jun Zhao & Manolis Roulis & Piotr Bielecki & Richard A. Flavell & Boaz Nadler & Yuval Kluger, 2022. "Zero-preserving imputation of single-cell RNA-seq data," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
- Shahin Mohammadi & Jose Davila-Velderrain & Manolis Kellis, 2020. "A multiresolution framework to characterize single-cell state landscapes," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
- Zhijian Li & Christoph Kuppe & Susanne Ziegler & Mingbo Cheng & Nazanin Kabgani & Sylvia Menzel & Martin Zenke & Rafael Kramann & Ivan G. Costa, 2021. "Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen," Nature Communications, Nature, vol. 12(1), pages 1-14, 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.
- Wei Vivian Li & Jingyi Jessica Li, 2018. "An accurate and robust imputation method scImpute for single-cell RNA-seq data," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
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