Scarf enables a highly memory-efficient analysis of large-scale single-cell genomics data
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DOI: 10.1038/s41467-022-32097-3
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- Dmitry Kobak & Philipp Berens, 2019. "The art of using t-SNE for single-cell transcriptomics," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
- Junyue Cao & Malte Spielmann & Xiaojie Qiu & Xingfan Huang & Daniel M. Ibrahim & Andrew J. Hill & Fan Zhang & Stefan Mundlos & Lena Christiansen & Frank J. Steemers & Cole Trapnell & Jay Shendure, 2019. "The single-cell transcriptional landscape of mammalian organogenesis," Nature, Nature, vol. 566(7745), pages 496-502, February.
- Jason D. Buenrostro & Beijing Wu & Ulrike M. Litzenburger & Dave Ruff & Michael L. Gonzales & Michael P. Snyder & Howard Y. Chang & William J. Greenleaf, 2015. "Single-cell chromatin accessibility reveals principles of regulatory variation," Nature, Nature, vol. 523(7561), pages 486-490, July.
- Betsabeh Khoramian Tusi & Samuel L. Wolock & Caleb Weinreb & Yung Hwang & Daniel Hidalgo & Rapolas Zilionis & Ari Waisman & Jun R. Huh & Allon M. Klein & Merav Socolovsky, 2018. "Population snapshots predict early haematopoietic and erythroid hierarchies," Nature, Nature, vol. 555(7694), pages 54-60, March.
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