11 References
专题介绍:单细胞RNA-seq被评为2018年重大科研进展,但实际上这是老技术。2015年,商品化单细胞RNA测序流程已经建立,成果发表在Cell上。今年井喷式发文章,关注点那么高,是因为最近这项技术全面商品化了。
Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman. 1990. “Basic Local Alignment Search Tool.” Journal of Molecular Biology 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 Bioinformatics 11 (1): 94. https://doi.org/10.1186/1471-2105-11-94.Buttner, Maren, Zhichao Miao, Alexander Wolf, Sarah A Teichmann, and Fabian J Theis. 2017. “Assessment of Batch-Correction Methods for scRNA-seq Data with a New Test Metric.” bioRxiv, October, 200345.Deng, Q., D. Ramskold, B. Reinius, and R. 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 Meth 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 Meth 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.” Bioinformatics, 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.” bioRxiv, May, 121202.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 Meth 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 Meth 6 (5): 377–82. https://doi.org/10.1038/nmeth.1315.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 (January): 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.” Molecular Cell 65 (4): 631–643.e4. https://doi.org/10.1016/j.molcel.2017.01.023.
专题:单细胞RNA-seq测序数据分析:
- 1 About the course 关于单细胞测序跟练课程
- 2 单细胞RNA-seq介绍
- 3 Processing Raw scRNA-Seq Sequencing Data: From Reads to a Count Matrix处理scRNA-seq测序的原始数据:把读取的数据转化为计数矩阵
- 5 scRNA-seq Analysis with Bioconductor
- 6 Basic Quality Control (QC) and Exploration of scRNA-seq Datasets
- 7 Biological Analysis
- 8 Single cell RNA-seq analysis using Seurat
- 9 scRNA-seq Dataset Integration
- 10 Resources
- 11 References
- 单细胞RNA-seq测序分析-跟练
- 谈谈单细胞测序那些事儿
- 【单细胞技术贴】空间转录组与单细胞转录组的整合分析(上篇)
- 【单细胞技术贴】空间转录组与单细胞转录组的整合分析(下篇)
- 【单细胞数据分析】SCENIC 从单细胞数据推断基因调控网络和细胞类型
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