Fast searches of large collections of single-cell data using scfind.
Nat Methods
; 18(3): 262-271, 2021 03.
Article
en En
| MEDLINE
| ID: mdl-33649586
ABSTRACT
Single-cell technologies have made it possible to profile millions of cells, but for these resources to be useful they must be easy to query and access. To facilitate interactive and intuitive access to single-cell data we have developed scfind, a single-cell analysis tool that facilitates fast search of biologically or clinically relevant marker genes in cell atlases. Using transcriptome data from six mouse cell atlases, we show how scfind can be used to evaluate marker genes, perform in silico gating, and identify both cell-type-specific and housekeeping genes. Moreover, we have developed a subquery optimization routine to ensure that long and complex queries return meaningful results. To make scfind more user friendly, we use indices of PubMed abstracts and techniques from natural language processing to allow for arbitrary queries. Finally, we show how scfind can be used for multi-omics analyses by combining single-cell ATAC-seq data with transcriptome data.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Almacenamiento y Recuperación de la Información
/
Análisis de la Célula Individual
/
Transcriptoma
/
Manejo de Datos
Límite:
Animals
Idioma:
En
Revista:
Nat Methods
Asunto de la revista:
TECNICAS E PROCEDIMENTOS DE LABORATORIO
Año:
2021
Tipo del documento:
Article
País de afiliación:
Reino Unido