Automated methods for cell type annotation on scRNA-seq data

Automated methods for cell type annotation on scRNA-seq data

The advent of single-cell sequencing started a new era of transcriptomic and genomic research, advancing our knowledge of the cellular heterogeneity and dynamics. Cell type annotation is a crucial step in analyzing single-cell RNA sequencing data, yet manual annotation is time-consuming and partiall...

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Bibliographic Details
Main Authors: Giovanni Pasquini, Jesus Eduardo Rojo Arias, Patrick Schäfer, Volker Busskamp
Format: Article
Language:English
Published: Elsevier 2021-01-01
Series:Computational and Structural Biotechnology Journal
Subjects:
scRNA-seq
Cell type
Cell state
Automatic annotation
Online Access:http://www.sciencedirect.com/science/article/pii/S2001037021000192
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spelling doaj-72c1e9c5fdbc4df8b56b7a5da34954962021-02-05T15:30:42ZengElsevierComputational and Structural Biotechnology Journal2001-03702021-01-0119961969Automated methods for cell type annotation on scRNA-seq dataGiovanni Pasquini0Jesus Eduardo Rojo Arias1Patrick Schäfer2Volker Busskamp3Technische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Dresden 01307, Germany; Universitäts-Augenklinik Bonn, University of Bonn, Department of Ophthalmology, Bonn 53127, GermanyWellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UKTechnische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Dresden 01307, GermanyTechnische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Dresden 01307, Germany; Universitäts-Augenklinik Bonn, University of Bonn, Department of Ophthalmology, Bonn 53127, Germany; Corresponding author at: Universitäts-Augenklinik Bonn, University of Bonn, Department of Ophthalmology, Bonn 53127, Germany.The advent of single-cell sequencing started a new era of transcriptomic and genomic research, advancing our knowledge of the cellular heterogeneity and dynamics. Cell type annotation is a crucial step in analyzing single-cell RNA sequencing data, yet manual annotation is time-consuming and partially subjective. As an alternative, tools have been developed for automatic cell type identification. Different strategies have emerged to ultimately associate gene expression profiles of single cells with a cell type either by using curated marker gene databases, correlating reference expression data, or transferring labels by supervised classification. In this review, we present an overview of the available tools and the underlying approaches to perform automated cell type annotations on scRNA-seq data.http://www.sciencedirect.com/science/article/pii/S2001037021000192scRNA-seqCell typeCell stateAutomatic annotation
collection DOAJ
language English
format Article
sources DOAJ
author Giovanni Pasquini
Jesus Eduardo Rojo Arias
Patrick Schäfer
Volker Busskamp
spellingShingle Giovanni Pasquini
Jesus Eduardo Rojo Arias
Patrick Schäfer
Volker Busskamp
Automated methods for cell type annotation on scRNA-seq data
Computational and Structural Biotechnology Journal
scRNA-seq
Cell type
Cell state
Automatic annotation
author_facet Giovanni Pasquini
Jesus Eduardo Rojo Arias
Patrick Schäfer
Volker Busskamp
author_sort Giovanni Pasquini
title Automated methods for cell type annotation on scRNA-seq data
title_short Automated methods for cell type annotation on scRNA-seq data
title_full Automated methods for cell type annotation on scRNA-seq data
title_fullStr Automated methods for cell type annotation on scRNA-seq data
title_full_unstemmed Automated methods for cell type annotation on scRNA-seq data
title_sort automated methods for cell type annotation on scrna-seq data
publisher Elsevier
series Computational and Structural Biotechnology Journal
issn 2001-0370
publishDate 2021-01-01
description The advent of single-cell sequencing started a new era of transcriptomic and genomic research, advancing our knowledge of the cellular heterogeneity and dynamics. Cell type annotation is a crucial step in analyzing single-cell RNA sequencing data, yet manual annotation is time-consuming and partially subjective. As an alternative, tools have been developed for automatic cell type identification. Different strategies have emerged to ultimately associate gene expression profiles of single cells with a cell type either by using curated marker gene databases, correlating reference expression data, or transferring labels by supervised classification. In this review, we present an overview of the available tools and the underlying approaches to perform automated cell type annotations on scRNA-seq data.
topic scRNA-seq
Cell type
Cell state
Automatic annotation
url http://www.sciencedirect.com/science/article/pii/S2001037021000192
work_keys_str_mv AT giovannipasquini automatedmethodsforcelltypeannotationonscrnaseqdata
AT jesuseduardorojoarias automatedmethodsforcelltypeannotationonscrnaseqdata
AT patrickschafer automatedmethodsforcelltypeannotationonscrnaseqdata
AT volkerbusskamp automatedmethodsforcelltypeannotationonscrnaseqdata
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