2024 updated single-cell guide - Part 1: RNA preprocessing and quality control
This is a comprehensive tutorial on the most up-to-date recommendations for single-cell sequencing. This is part 1 of a multi-part series. Here I download a dataset, remove background RNA, preform quality control, and remove low quality cells. Part 2 will cover dimension reduction and cell annotation. We will eventually get to in-depth analysis and scATAC analysis. Notebook: https://github.com/mousepixels/sanbom... Paper/dataset: https://www.cell.com/cancer-cell/full... Reference: https://www.sc-best-practices.org/pre... 0:00 Intro 0:27 Setup 12:08 Cellbender 18:20 QC 28:05 preprocessing 39:42 Conclusions
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2024 updated single-cell guide - Part 2: RNA Integration and annotation
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