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Best practices
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Current best practices in single‐cell RNA‐seq analysis: a tutorial | Molecular Systems Biology www.embopress.org
https://www.embopress.org/doi/full/10.15252/msb.20188746

Slightly outdated now but still a really good reference for the core concepts and steps in a scRNA-seq analysis workflow

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Project structure djnavarro.net
https://djnavarro.net/slides-project-structure
  • Good summary of best practices for naming/ordering files
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Single-cell best practices — Single-cell best practices www.sc-best-practices.org
https://www.sc-best-practices.org/preamble.html

Really comprehensive book on scRNA-seq background and analysis using ScanPy/scverse

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