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Review
. 2021 Jun;16(6):2749-2764.
doi: 10.1038/s41596-021-00534-0. Epub 2021 May 24.

Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods

Zoe A Clarke #  1   2 , Tallulah S Andrews #  2   3   4 , Jawairia Atif #  3   4 , Delaram Pouyabahar #  1   2 , Brendan T Innes  1   2 , Sonya A MacParland  5   6   7 , Gary D Bader  8   9   10   11
Affiliations
Review

Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods

Zoe A Clarke et al. Nat Protoc. 2021 Jun.

Abstract

Single-cell transcriptomics can profile thousands of cells in a single experiment and identify novel cell types, states and dynamics in a wide variety of tissues and organisms. Standard experimental protocols and analysis workflows have been developed to create single-cell transcriptomic maps from tissues. This tutorial focuses on how to interpret these data to identify cell types, states and other biologically relevant patterns with the objective of creating an annotated map of cells. We recommend a three-step workflow including automatic cell annotation (wherever possible), manual cell annotation and verification. Frequently encountered challenges are discussed, as well as strategies to address them. Guiding principles and specific recommendations for software tools and resources that can be used for each step are covered, and an R notebook is included to help run the recommended workflow. Basic familiarity with computer software is assumed, and basic knowledge of programming (e.g., in the R language) is recommended.

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References

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