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

Tallulah S. Andrews, Zoe A. Clarke, Jawairia Atif, Delaram Pouyabahar, Brendan T. Innes, Sonya A. MacParland, Gary D. Bader

Published: 2021-05-23 DOI: 10.1038/s41596-021-00534-0

single-cell transcriptomics

workflow

cell annotation

R notebook

software tools

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Author Correction: Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq

Generation of heart-forming organoids from human pluripotent stem cells

Design and fabrication of wearable electronic textiles using twisted fiber-based threads

Activation of mechanoluminescent nanotransducers by focused ultrasound enables light delivery to deep-seated tissue in vivo

Chromatin accessibility profiling by ATAC-seq

Deoxyfluorination of phenols for chemoselective18F-labeling of peptides

Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA

Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids

An inexpensive semi-automated sample processing pipeline for cell-free RNA extraction

Application of CHyMErA Cas9-Cas12a combinatorial genome-editing platform for genetic interaction mapping and gene fragment deletion screening

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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
Main
Step 1: automatic cell annotation
Step 2: expert manual cell annotation
- Annotating cell states and gradients
Step 3: annotation verification
Experimental design considerations
- The impact of experimental and analysis parameters on annotation
- Workflow recommendations
Concluding remarks
- References
- References
References
ACKNOWLEDGMENTS

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

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