How to perform PCA on single-cell RNA-Seq data in three simple steps

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DOI of this video (for citations): doi.org/10.528...
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References:
Batson, Joshua, Loïc Royer, and James Webber. “Molecular Cross-Validation for Single-Cell RNA-Seq.” BioRxiv, September 30, 2019, 786269. doi.org/10.110....
Grün, Dominic, Lennart Kester, and Alexander van Oudenaarden. “Validation of Noise Models for Single-Cell Transcriptomics.” Nature Methods 11, no. 6 (June 2014): 637-40. doi.org/10.103....
Hafemeister, Christoph, and Rahul Satija. “Normalization and Variance Stabilization of Single-Cell RNA-Seq Data Using Regularized Negative Binomial Regression.” Genome Biology 20, no. 1 (23 2019): 296. doi.org/10.118....
Hsu, Lauren L., and Aedin C. Culhane. “Impact of Data Preprocessing on Integrative Matrix Factorization of Single Cell Data.” Frontiers in Oncology 10 (2020). doi.org/10.338....
Sun, Shiquan, Jiaqiang Zhu, Ying Ma, and Xiang Zhou. “Accuracy, Robustness and Scalability of Dimensionality Reduction Methods for Single-Cell RNA-Seq Analysis.” Genome Biology 20, no. 1 (10 2019): 269. doi.org/10.118....
Townes, F. William, Stephanie C. Hicks, Martin J. Aryee, and Rafael A. Irizarry. “Feature Selection and Dimension Reduction for Single-Cell RNA-Seq Based on a Multinomial Model.” Genome Biology 20, no. 1 (23 2019): 295. doi.org/10.118....
Tsuyuzaki, Koki, Hiroyuki Sato, Kenta Sato, and Itoshi Nikaido. “Benchmarking Principal Component Analysis for Large-Scale Single-Cell RNA-Sequencing.” Genome Biology 21, no. 1 (20 2020): 9. doi.org/10.118....
Wagner, Florian, Dalia Barkley, and Itai Yanai. “Accurate Denoising of Single-Cell RNA-Seq Data Using Unbiased Principal Component Analysis.” BioRxiv, June 17, 2019, 655365. doi.org/10.110....
Wagner, Florian. “Monet: An Open-Source Python Package for Analyzing and Integrating ScRNA-Seq Data Using PCA-Based Latent Spaces.” BioRxiv, 2020. doi.org/10.110....

[@黄梓煊-g9u]

Really great video, thanks a lot for explaining PCA so well in such a concise way

[@mikelawrence5507]

Nice summary for reasoning behind workflow! I was looking for an example of PCA but only saw t-SNEs

[@jattpigeonscorner9368]

Great Content. Please keep uploading

[@ilyasimutin]

Thank you, great lecture!

[@diraczhu9347]

Great video, it helps !

[@pariaalipour61]

Thanks for the great video. I have a question regarding scaling step; in the scaling step as you mentioned we shouldn't multiply by like a million and the number is median/total umi count. In Seurat NormalizeData function does divide the count by total cell count and multiply to 10000 scale factor. I was wondering what is the difference?

[@derricmorgan2282]

Nice video, thanks!

[@derricmorgan2282]

the only thing is the sound quality, I had to adjust volume and the sound is a bit rattling.

[@derricmorgan2282]

so nice that you included the links, the papers are really interesting