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Dual indexed library design enables compatibility of in-Drop single-cell RNA-sequencing with exAMP chemistry sequencing platforms
BackgroundThe increasing demand of single-cell RNA-sequencing (scRNA-seq) experiments, such as the number of experiments and cells queried per...
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A new and effective two-step clustering approach for single cell RNA sequencing data
BackgroundThe rapid devolvement of single cell RNA sequencing (scRNA-seq) technology leads to huge amounts of scRNA-seq data, which greatly advance...
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DISCERN: deep single-cell expression reconstruction for improved cell clustering and cell subtype and state detection
BackgroundSingle-cell sequencing provides detailed insights into biological processes including cell differentiation and identity. While providing...
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scPML: pathway-based multi-view learning for cell type annotation from single-cell RNA-seq data
Recent developments in single-cell technology have enabled the exploration of cellular heterogeneity at an unprecedented level, providing invaluable...
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A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data
Automatic cell type annotation methods are increasingly used in single-cell RNA sequencing (scRNA-seq) analysis due to their fast and precise...
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Single-cell RNA sequencing technology in human spermatogenesis: Progresses and perspectives
Spermatogenesis, a key part of the spermiation process, is regulated by a combination of key cells, such as primordial germ cells, spermatogonial...
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Single-cell transcriptomics: background, technologies, applications, and challenges
Single-cell sequencing was developed as a high-throughput tool to elucidate unusual and transient cell states that are barely visible in the bulk....
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Single-Cell Analysis of the Transcriptome and Epigenome
Epigenome regulation has emerged as an important mechanism for the maintenance of organ function in health and disease. Dissecting epigenomic...
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Comparative analysis of cell–cell communication at single-cell resolution
Inference of cell–cell communication from single-cell RNA sequencing data is a powerful technique to uncover intercellular communication pathways,...
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scFSNN: a feature selection method based on neural network for single-cell RNA-seq data
While single-cell RNA sequencing (scRNA-seq) allows researchers to analyze gene expression in individual cells, its unique characteristics like...
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scSemiAAE: a semi-supervised clustering model for single-cell RNA-seq data
BackgroundSingle-cell RNA sequencing (scRNA-seq) strives to capture cellular diversity with higher resolution than bulk RNA sequencing. Clustering...
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ProBac-seq, a bacterial single-cell RNA sequencing methodology using droplet microfluidics and large oligonucleotide probe sets
Methods that measure the transcriptomic state of thousands of individual cells have transformed our understanding of cellular heterogeneity in...
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Transcriptomics at the Single Cell Level and Human Diseases: Opportunities and Challenges in Data Processing and Analysis
Despite breakthroughs in precision medicine during the past decade due to bulk RNA profiling approaches, those conceal gene expression heterogeneity...
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Transcriptome Analysis Using RNA-seq and scRNA-seq
Differential gene expression profile is a powerful tool to identify changes in cell or tissue transcriptomes. It allows understanding complex...
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iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks
The integration of single-cell RNA-sequencing datasets from multiple sources is critical for deciphering cell-to-cell heterogeneities and...
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Integrative insights and clinical applications of single-cell sequencing in cancer immunotherapy
Recently, immunotherapy has gained increasing popularity in oncology. Several immunotherapies obtained remarkable clinical effects, but the efficacy...
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Single-Cell RNA Sequencing Analysis: A Step-by-Step Overview
Thanks to innovative sample-preparation and sequencing technologies, gene expression in individual cells can now be measured for thousands of cells...
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Profiling RNA Editing in Single Cells
RNA editing is a widespread molecular phenomenon occurring in a variety of organisms. In humans, it mainly involves the deamination of adenosine to...
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The killifish germline regulates longevity and somatic repair in a sex-specific manner
Classical evolutionary theories propose tradeoffs among reproduction, damage repair and lifespan. However, the specific role of the germline in...
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Understanding plant pathogen interactions using spatial and single-cell technologies
Plants are in contact with diverse pathogens and microorganisms. Intense investigation over the last 30 years has resulted in the identification of...
