References

Workflows and data formats

• 10x Genomics. What is Cell Ranger?
• 10x Genomics. Cell Ranger gene-expression algorithm
• Scanpy. Preprocessing and clustering tutorial
• Seurat. Guided clustering tutorial
• Wolf FA, Angerer P, Theis FJ. SCANPY: large-scale single-cell gene expression data analysis. Genome Biology. 2018.
• Stuart T, et al. Comprehensive integration of single-cell data. Cell. 2019.

Analysis methods and cautions

• Luecken MD, Theis FJ. Current best practices in single-cell RNA-seq analysis. Molecular Systems Biology. 2019.
• Lun ATL, et al. EmptyDrops: distinguishing cells from empty droplets. Genome Biology. 2019.
• Wolock SL, Lopez R, Klein AM. Scrublet: computational identification of cell doublets. Cell Systems. 2019.
• Traag VA, Waltman L, van Eck NJ. From Louvain to Leiden: guaranteeing well-connected communities. Scientific Reports. 2019.
• McInnes L, Healy J, Melville J. UMAP: Uniform Manifold Approximation and Projection. 2018.
• Hafemeister C, Satija R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biology. 2019.
• Squair JW, et al. Confronting false discoveries in single-cell differential expression. Nature Communications. 2021.
• Amezquita RA, et al. Orchestrating single-cell analysis with Bioconductor. Nature Methods. 2020.

How to use these references

Documentation links describe current software behavior and can change with versions. Papers describe methods and evidence at publication time. Record the software version actually used, read method-specific documentation, and do not substitute this book for protocol, statistical, clinical, privacy, or regulatory review.