Single-cell Mayo Map (scMayoMap): an easy-to-use tool for cell type annotation in single-cell RNA-sequencing data analysis.
Cell type annotation
Cell type markers
Single-cell RNA-sequencing
scMayoMap
scMayoMapDatabase
Journal
BMC biology
ISSN: 1741-7007
Titre abrégé: BMC Biol
Pays: England
ID NLM: 101190720
Informations de publication
Date de publication:
20 10 2023
20 10 2023
Historique:
received:
13
09
2023
accepted:
06
10
2023
medline:
23
10
2023
pubmed:
20
10
2023
entrez:
20
10
2023
Statut:
epublish
Résumé
Single-cell RNA-sequencing (scRNA-seq) has become a widely used tool for both basic and translational biomedical research. In scRNA-seq data analysis, cell type annotation is an essential but challenging step. In the past few years, several annotation tools have been developed. These methods require either labeled training/reference datasets, which are not always available, or a list of predefined cell subset markers, which are subject to biases. Thus, a user-friendly and precise annotation tool is still critically needed. We curated a comprehensive cell marker database named scMayoMapDatabase and developed a companion R package scMayoMap, an easy-to-use single-cell annotation tool, to provide fast and accurate cell type annotation. The effectiveness of scMayoMap was demonstrated in 48 independent scRNA-seq datasets across different platforms and tissues. Additionally, the scMayoMapDatabase can be integrated with other tools and further improve their performance. scMayoMap and scMayoMapDatabase will help investigators to define the cell types in their scRNA-seq data in a streamlined and user-friendly way.
Sections du résumé
BACKGROUND
Single-cell RNA-sequencing (scRNA-seq) has become a widely used tool for both basic and translational biomedical research. In scRNA-seq data analysis, cell type annotation is an essential but challenging step. In the past few years, several annotation tools have been developed. These methods require either labeled training/reference datasets, which are not always available, or a list of predefined cell subset markers, which are subject to biases. Thus, a user-friendly and precise annotation tool is still critically needed.
RESULTS
We curated a comprehensive cell marker database named scMayoMapDatabase and developed a companion R package scMayoMap, an easy-to-use single-cell annotation tool, to provide fast and accurate cell type annotation. The effectiveness of scMayoMap was demonstrated in 48 independent scRNA-seq datasets across different platforms and tissues. Additionally, the scMayoMapDatabase can be integrated with other tools and further improve their performance.
CONCLUSIONS
scMayoMap and scMayoMapDatabase will help investigators to define the cell types in their scRNA-seq data in a streamlined and user-friendly way.
Identifiants
pubmed: 37858214
doi: 10.1186/s12915-023-01728-6
pii: 10.1186/s12915-023-01728-6
pmc: PMC10588107
doi:
Substances chimiques
RNA
63231-63-0
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
223Subventions
Organisme : NHGRI NIH HHS
ID : R21 HG011662
Pays : United States
Organisme : NIA NIH HHS
ID : U54 AG079754
Pays : United States
Organisme : NIA NIH HHS
ID : U54 AG044170
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM144351
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG055529
Pays : United States
Organisme : NIA NIH HHS
ID : P01 AG062413
Pays : United States
Commentaires et corrections
Type : UpdateOf
Informations de copyright
© 2023. BioMed Central Ltd., part of Springer Nature.
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