A universal deep neural network for in-depth cleaning of single-cell RNA-Seq data
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DOI: 10.1038/s41467-022-29576-y
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- 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.
- Lawrence Hubert & Phipps Arabie, 1985. "Comparing partitions," Journal of Classification, Springer;The Classification Society, vol. 2(1), pages 193-218, 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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