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Accurately Deciphering Novel Cell Type in Spatially Resolved Single-Cell Data Through Optimal Transport
Recent advances in spatial transcriptomics enable the detection of spatial heterogeneity at single-cell resolution. However, existing annotation...
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scMD facilitates cell type deconvolution using single-cell DNA methylation references
The proliferation of single-cell RNA-sequencing data has led to the widespread use of cellular deconvolution, aiding the extraction of...
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Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data
The origin and evolution of cell types has emerged as a key topic in evolutionary biology. Driven by rapidly accumulating single-cell datasets,...
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CHLPCA: Correntropy-Based Hypergraph Regularized Sparse PCA for Single-Cell Type Identification
Over the past decade, high-throughput sequencing technologies have driven a dramatic increase in single-cell RNA sequencing (scRNA-seq) data. The...
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Single Cell Analysis Methods and Protocols
This volume explores the latest advancements and techniques used to study cell analysis, their capabilities, and the type of results that can be...
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Single-cell Mayo Map (scMayoMap): an easy-to-use tool for cell type annotation in single-cell RNA-sequencing data analysis
BackgroundSingle-cell RNA-sequencing (scRNA-seq) has become a widely used tool for both basic and translational biomedical research. In scRNA-seq...
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Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis
Here we demonstrate that the large language model GPT-4 can accurately annotate cell types using marker gene information in single-cell RNA...
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Multiple Cell Lineages Give Rise to a Cell Type
It has long been assumed that a specific cell type arises following stepwise specification of cells corresponding to the branching of cell lineages....
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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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Regulation of endocrine cell alternative splicing revealed by single-cell RNA sequencing in type 2 diabetes pathogenesis
The prevalent RNA alternative splicing (AS) contributes to molecular diversity, which has been demonstrated in cellular function regulation and...
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Tumor cell type and gene marker identification by single layer perceptron neural network on single-cell RNA sequence data
Tumors have drawn increasing attention recently because of their heterogeneous interior structures. Particularly, single-cell RNA (scRNA) mechanics...
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Cell-Type Deconvolution of Bulk DNA Methylation Data with EpiSCORE
DNA methylation data generated from bulk tissue represents a mixture of many different cell types. Variation in the cell-type composition of tissues...
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ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering
MotivationCategorizing cells into distinct types can shed light on biological tissue functions and interactions, and uncover specific mechanisms...
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GTM-decon: guided-topic modeling of single-cell transcriptomes enables sub-cell-type and disease-subtype deconvolution of bulk transcriptomes
Cell-type composition is an important indicator of health. We present Guided Topic Model for deconvolution (GTM-decon) to automatically infer...
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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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Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters
The inability to scalably and precisely measure the activity of developmental cis -regulatory elements (CREs) in multicellular systems is a bottleneck...
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Time series single-cell transcriptional atlases reveal cell fate differentiation driven by light in Arabidopsis seedlings
Light serves as the energy source for plants as well as a signal for growth and development during their whole life cycle. Seedling de-etiolation is...
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SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data
Quality control (QC) is a critical component of single-cell RNA-seq (scRNA-seq) processing pipelines. Current approaches to QC implicitly assume that...
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Updated single cell reference atlas for the starlet anemone Nematostella vectensis
BackgroundThe recent combination of genomics and single cell transcriptomics has allowed to assess a variety of non-conventional model organisms in...
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A single cell RNA sequence atlas of the early Drosophila larval eye
The Drosophila eye has been an important model to understand principles of differentiation, proliferation, apoptosis and tissue morphogenesis....
