11 References

Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman. 1990. “Basic Local Alignment Search Tool.” J. Mol. Biol. 215 (3): 403–10. https://doi.org/10.1016/s0022-2836(05)80360-2.

Anders, Simon, and Wolfgang Huber. 2010. “Differential Expression Analysis for Sequence Count Data.” Genome Biol. 11 (10): R106. https://doi.org/10.1186/gb-2010-11-10-r106.

Archer, Nathan, Mark D. Walsh, Vahid Shahrezaei, and Daniel Hebenstreit. 2016. “Modeling Enzyme Processivity Reveals That RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways.” Cell Systems 3 (5): 467–479.e12. https://doi.org/10.1016/j.cels.2016.10.012.

Bullard, James H, Elizabeth Purdom, Kasper D Hansen, and Sandrine Dudoit. 2010. “Evaluation of Statistical Methods for Normalization and Differential Expression in mRNA-Seq Experiments.” BMC Bioinf. 11 (1): 94. https://doi.org/10.1186/1471-2105-11-94.

Büttner, Maren, Zhichao Miao, F. Alexander Wolf, Sarah A. Teichmann, and Fabian J. Theis. 2018. “A Test Metric for Assessing Single-Cell RNA-Seq Batch Correction.” Nat. Methods 16 (1): 43–49. https://doi.org/10.1038/s41592-018-0254-1.

Deng, Qiaolin, Daniel Ramsköld, Björn Reinius, and Rickard Sandberg. 2014. “Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells.” Science 343 (6167): 193–96. https://doi.org/10.1126/science.1245316.

Guo, Minzhe, Hui Wang, S. Steven Potter, Jeffrey A. Whitsett, and Yan Xu. 2015. “SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis.” PLOS Comput. Biol. 11 (11): e1004575. https://doi.org/10.1371/journal.pcbi.1004575.

Kharchenko, Peter V, Lev Silberstein, and David T Scadden. 2014. “Bayesian Approach to Single-Cell Differential Expression Analysis.” Nat. Methods 11 (7): 740–42. https://doi.org/10.1038/nmeth.2967.

Kiselev, Vladimir Yu, Kristina Kirschner, Michael T Schaub, Tallulah Andrews, Andrew Yiu, Tamir Chandra, Kedar N Natarajan, et al. 2017. “Sc3: Consensus Clustering of Single-Cell RNA-Seq Data.” Nat. Methods 14 (5): 483–86. https://doi.org/10.1038/nmeth.4236.

L. Lun, Aaron T., Karsten Bach, and John C. Marioni. 2016. “Pooling Across Cells to Normalize Single-Cell RNA Sequencing Data with Many Zero Counts.” Genome Biol. 17 (1). https://doi.org/10.1186/s13059-016-0947-7.

Levine, Jacob H., Erin F. Simonds, Sean C. Bendall, Kara L. Davis, El-ad D. Amir, Michelle D. Tadmor, Oren Litvin, et al. 2015. “Data-Driven Phenotypic Dissection of AML Reveals Progenitor-Like Cells That Correlate with Prognosis.” Cell 162 (1): 184–97. https://doi.org/10.1016/j.cell.2015.05.047.

McCarthy, Davis J., Kieran R. Campbell, Aaron T. L. Lun, and Quin F. Wills. 2017. “Scater: Pre-Processing, Quality Control, Normalization and Visualization of Single-Cell RNA-Seq Data in r.” Method. Biochem. Anal., January, btw777. https://doi.org/10.1093/bioinformatics/btw777.

Regev, Aviv, Sarah Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, et al. 2017. “The Human Cell Atlas.” eLife 6 (December): 121202. https://doi.org/10.7554/elife.27041.

Robinson, Mark D, and Alicia Oshlack. 2010. “A Scaling Normalization Method for Differential Expression Analysis of RNA-Seq Data.” Genome Biol. 11 (3): R25. https://doi.org/10.1186/gb-2010-11-3-r25.

Svensson, Valentine, Kedar Nath Natarajan, Lam-Ha Ly, Ricardo J Miragaia, Charlotte Labalette, Iain C Macaulay, Ana Cvejic, and Sarah A Teichmann. 2017. “Power Analysis of Single-Cell RNA-Sequencing Experiments.” Nat. Methods 14 (4): 381–87. https://doi.org/10.1038/nmeth.4220.

Tang, Fuchou, Catalin Barbacioru, Yangzhou Wang, Ellen Nordman, Clarence Lee, Nanlan Xu, Xiaohui Wang, et al. 2009. “mRNA-Seq Whole-Transcriptome Analysis of a Single Cell.” Nat. Methods 6 (5): 377–82. https://doi.org/10.1038/nmeth.1315.

The Tabula Muris Consortium., Logistical coordination. et al., Overall coordination. 2018. “Single-Cell Transcriptomics of 20 Mouse Organs Creates a Tabula Muris.” Nature 562 (7727): 367–72. https://doi.org/10.1038/s41586-018-0590-4.

Tung, Po-Yuan, John D. Blischak, Chiaowen Joyce Hsiao, David A. Knowles, Jonathan E. Burnett, Jonathan K. Pritchard, and Yoav Gilad. 2017. “Batch Effects and the Effective Design of Single-Cell Gene Expression Studies.” Sci. Rep. 7 (1): 39921. https://doi.org/10.1038/srep39921.

Wickham, Hadley. 2014. “Tidy Data.” J. Stat. Softw. 59 (10). https://doi.org/10.18637/jss.v059.i10.

Ziegenhain, Christoph, Beate Vieth, Swati Parekh, Björn Reinius, Amy Guillaumet-Adkins, Martha Smets, Heinrich Leonhardt, Holger Heyn, Ines Hellmann, and Wolfgang Enard. 2017. “Comparative Analysis of Single-Cell RNA Sequencing Methods.” Mol. Cell 65 (4): 631–643.e4. https://doi.org/10.1016/j.molcel.2017.01.023.