scNAT: a deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles
Biqing Zhu, Yuge Wang, Li-Ting Ku, David van Dijk, Le Zhang, David A. Hafler, Hongyu Zhao
Abstract
Many deep learning-based methods have been proposed to handle complex single-cell data. Deep learning approaches may also prove useful to jointly analyze single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scTCR-seq) data for novel discoveries. We developed scNAT, a deep learning method that integrates paired scRNA-seq and scTCR-seq data to represent data in a unified latent space for downstream analysis. We demonstrate that scNAT is capable of removing batch effects, and identifying cell clusters and a T cell migration trajectory from blood to cerebrospinal fluid in multiple sclerosis.
Topics & Concepts
BiologySingle cell sequencingComputational biologyDeep sequencingRNA-SeqDeep learningCellRNADNA sequencingArtificial intelligenceGeneticsComputer scienceDNAExome sequencingGeneMutationGenomeTranscriptomeGene expressionSingle-cell and spatial transcriptomicsT-cell and B-cell ImmunologyNeuroinflammation and Neurodegeneration Mechanisms