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   Articles with "type annotation" as a keyword



scGAA: a general gated axial-attention model for accurate cell-type annotation of single-cell RNA-seq data

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recommendations! Published in 2024 at "Scientific Reports"

DOI: 10.1038/s41598-024-73356-1

Abstract: Single-cell RNA sequencing (scRNA-seq) is a key technology for investigating cell development and analysing cell diversity across various diseases. However, the high dimensionality and extreme sparsity of scRNA-seq data pose great challenges for accurate cell… read more here.

Keywords: type annotation; attention; cell; model ... See more keywords

Evaluation of cell type annotation reliability using a large language model-based identifier

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recommendations! Published in 2025 at "Communications Biology"

DOI: 10.1038/s42003-025-08745-x

Abstract: Ensuring accurate cell type annotation in single-cell RNA sequencing data is a significant challenge, as both expert and automated methods can be biased or constrained by their training data, leading to errors and time-consuming revisions.… read more here.

Keywords: type annotation; language; cell; model ... See more keywords

scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets.

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recommendations! Published in 2023 at "Briefings in bioinformatics"

DOI: 10.1093/bib/bbad179

Abstract: Undoubtedly, single-cell RNA sequencing (scRNA-seq) has changed the research landscape by providing insights into heterogeneous, complex and rare cell populations. Given that more such data sets will become available in the near future, their accurate… read more here.

Keywords: cell; type annotation; data sets; cell type ... See more keywords
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CIForm as a Transformer-based model for cell-type annotation of large-scale single-cell RNA-seq data.

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recommendations! Published in 2023 at "Briefings in bioinformatics"

DOI: 10.1093/bib/bbad195

Abstract: Single-cell omics technologies have made it possible to analyze the individual cells within a biological sample, providing a more detailed understanding of biological systems. Accurately determining the cell type of each cell is a crucial… read more here.

Keywords: cell; single cell; type annotation; cell type ... See more keywords

scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network.

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recommendations! Published in 2021 at "Nucleic acids research"

DOI: 10.1093/nar/gkab775

Abstract: Advances in single-cell RNA sequencing (scRNA-seq) have furthered the simultaneous classification of thousands of cells in a single assay based on transcriptome profiling. In most analysis protocols, single-cell type annotation relies on marker genes or… read more here.

Keywords: single cell; cell; type annotation; scdeepsort ... See more keywords

A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data

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recommendations! Published in 2022 at "Communications Biology"

DOI: 10.1101/2022.06.22.497193

Abstract: Cell type annotation is critical to understand the cell population heterogeneity in the single-cell RNA sequencing (scRNA-seq) analysis. Due to their fast, precise, and user-friendly advantages, automatic annotation methods are gradually replacing traditional unsupervised clustering… read more here.

Keywords: cell; type annotation; rare cell; scbalance ... See more keywords

gCAnno: a graph-based single cell type annotation method

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recommendations! Published in 2020 at "BMC Genomics"

DOI: 10.1186/s12864-020-07223-4

Abstract: Background Current single cell analysis methods annotate cell types at cluster-level rather than ideally at single cell level. Multiple exchangeable clustering methods and many tunable parameters have a substantial impact on the clustering outcome, often… read more here.

Keywords: single cell; type annotation; cell; cell type ... See more keywords

Consensus representation of multiple cell–cell graphs from gene signaling pathways for cell type annotation

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recommendations! Published in 2025 at "BMC Biology"

DOI: 10.1186/s12915-025-02128-8

Abstract: Recent advancements in single-cell RNA sequencing have greatly expanded our knowledge of the heterogeneous nature of tissues. However, robust and accurate cell type annotation continues to be a major challenge, hindered by issues such as… read more here.

Keywords: consensus; type annotation; cell; gene ... See more keywords

scTrans: Sparse attention powers fast and accurate cell type annotation in single-cell RNA-seq data

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recommendations! Published in 2025 at "PLOS Computational Biology"

DOI: 10.1371/journal.pcbi.1012904

Abstract: Cell type annotation is crucial in single-cell RNA sequencing data analysis because it enables significant biological discoveries and deepens our understanding of tissue biology. Given the high-dimensional and highly sparse nature of single-cell RNA sequencing… read more here.

Keywords: type annotation; single cell; biology; cell ... See more keywords

WCSGNet: a graph neural network approach using weighted cell-specific networks for cell-type annotation in scRNA-seq

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recommendations! Published in 2025 at "Frontiers in Genetics"

DOI: 10.3389/fgene.2025.1553352

Abstract: Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for understanding cellular heterogeneity, providing unprecedented resolution in molecular regulation analysis. Existing supervised learning approaches for cell type annotation primarily utilize gene expression profiles from… read more here.

Keywords: type annotation; cell; network; scrna seq ... See more keywords

French error type annotation for dictation: A platform with automatic error type annotation for French dictation exercises

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recommendations! Published in 2023 at "Frontiers in Psychology"

DOI: 10.3389/fpsyg.2022.1075932

Abstract: Dictation is considered an efficient exercise for testing the language proficiency of learners of French as a Foreign Language (FFL). However, the traditional teaching approach to dictation reduces the instructional feedback efficiency. To remedy this,… read more here.

Keywords: dictation; error; type annotation; error type ... See more keywords