A versatile and scalable single-cell data integration algorithm based on domain-adversarial and variational approximation.
Brief Bioinform
; 23(1)2022 01 17.
Article
em En
| MEDLINE
| ID: mdl-34585247
ABSTRACT
Single-cell technologies provide us new ways to profile transcriptomic landscape, chromatin accessibility, spatial expression patterns in heterogeneous tissues at the resolution of single cell. With enormous generated single-cell datasets, a key analytic challenge is to integrate these datasets to gain biological insights into cellular compositions. Here, we developed a domain-adversarial and variational approximation, DAVAE, which can integrate multiple single-cell datasets across samples, technologies and modalities with a single strategy. Besides, DAVAE can also integrate paired data of ATAC profile and transcriptome profile that are simultaneously measured from a same cell. With a mini-batch stochastic gradient descent strategy, it is scalable for large-scale data and can be accelerated by GPUs. Results on seven real data integration applications demonstrated the effectiveness and scalability of DAVAE in batch-effect removing, transfer learning and cell-type predictions for multiple single-cell datasets across samples, technologies and modalities. Availability:
DAVAE has been implemented in a toolkit package "scbean" in the pypi repository, and the source code can be also freely accessible at https//github.com/jhu99/scbean. All our data and source code for reproducing the results of this paper can be accessible at https//github.com/jhu99/davae_paper.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Análise de Célula Única
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
Brief Bioinform
Assunto da revista:
BIOLOGIA
/
INFORMATICA MEDICA
Ano de publicação:
2022
Tipo de documento:
Article
País de afiliação:
China