Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoder.
Brief Bioinform
; 24(3)2023 05 19.
Article
in En
| MEDLINE
| ID: mdl-37088976
ABSTRACT
Single-cell RNA sequencing (scRNA-seq) is a revolutionary breakthrough that determines the precise gene expressions on individual cells and deciphers cell heterogeneity and subpopulations. However, scRNA-seq data are much noisier than traditional high-throughput RNA-seq data because of technical limitations, leading to many scRNA-seq data studies about dimensionality reduction and visualization remaining at the basic data-stacking stage. In this study, we propose an improved variational autoencoder model (termed DREAM) for dimensionality reduction and a visual analysis of scRNA-seq data. Here, DREAM combines the variational autoencoder and Gaussian mixture model for cell type identification, meanwhile explicitly solving 'dropout' events by introducing the zero-inflated layer to obtain the low-dimensional representation that describes the changes in the original scRNA-seq dataset. Benchmarking comparisons across nine scRNA-seq datasets show that DREAM outperforms four state-of-the-art methods on average. Moreover, we prove that DREAM can accurately capture the expression dynamics of human preimplantation embryonic development. DREAM is implemented in Python, freely available via the GitHub website, https//github.com/Crystal-JJ/DREAM.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Single-Cell Analysis
/
Single-Cell Gene Expression Analysis
Limits:
Humans
Language:
En
Journal:
Brief Bioinform
Journal subject:
BIOLOGIA
/
INFORMATICA MEDICA
Year:
2023
Type:
Article
Affiliation country:
China