EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics.
Gigascience
; 13(1)2024 01 02.
Article
en En
| MEDLINE
| ID: mdl-38373746
ABSTRACT
BACKGROUND:
The emergence of high-resolved spatial transcriptomics (ST) has facilitated the research of novel methods to investigate biological development, organism growth, and other complex biological processes. However, high-resolved and whole transcriptomics ST datasets require customized imputation methods to improve the signal-to-noise ratio and the data quality.FINDINGS:
We propose an efficient and adaptive Gaussian smoothing (EAGS) imputation method for high-resolved ST. The adaptive 2-factor smoothing of EAGS creates patterns based on the spatial and expression information of the cells, creates adaptive weights for the smoothing of cells in the same pattern, and then utilizes the weights to restore the gene expression profiles. We assessed the performance and efficiency of EAGS using simulated and high-resolved ST datasets of mouse brain and olfactory bulb.CONCLUSIONS:
Compared with other competitive methods, EAGS shows higher clustering accuracy, better biological interpretations, and significantly reduced computational consumption.Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Imagen por Resonancia Magnética
/
Transcriptoma
Límite:
Animals
Idioma:
En
Revista:
Gigascience
Año:
2024
Tipo del documento:
Article
País de afiliación:
China
Pais de publicación:
Estados Unidos