ArticleGenome biology2019
CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Single-cell transcriptome analysis of stem cells from human exfoliated deciduous teeth investigating functional heterogeneity in immunomodulation.Scientific reports · 2024Article
- scMTD: a statistical multidimensional imputation method for single-cell RNA-seq data leveraging transcriptome dynamic information.Cell & bioscience · 2022Article
- Article
- Fast searches of large collections of single-cell data using scfind.Nature methods · 2021Article
- Automatic cell type identification methods for single-cell RNA sequencing.Computational and structural biotechnology journal · 2021Review
- Using DenseFly algorithm for cell searching on massive scRNA-seq datasets.BMC genomics · 2020Article
- Learning for single-cell assignment.Science advances · 2020Article
- Evaluation of single-cell classifiers for single-cell RNA sequencing data sets.Briefings in bioinformatics · 2020Review
- Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST.Nature communications · 2020Article
- Eleven grand challenges in single-cell data science.Genome biology · 2020Review
- Benchmarking principal component analysis for large-scale single-cell RNA-sequencing.Genome biology · 2020Article
- Next-generation computational tools for interrogating cancer immunity.Nature reviews. Genetics · 2019Review
- Challenges in unsupervised clustering of single-cell RNA-seq data.Nature reviews. Genetics · 2019Review
- CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing.Genome biology · 2019Article
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Authors and funding
4 authors.
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Abstract
Recent technical improvements in single-cell RNA sequencing (scRNA-seq) have enabled massively parallel profiling of transcriptomes, thereby promoting large-scale studies encompassing a wide range of cell types of multicellular organisms. With this background, we propose CellFishing.jl, a new method for searching atlas-scale datasets for similar cells and detecting noteworthy genes of query cells with high accuracy and throughput. Using multiple scRNA-seq datasets, we validate that our method demonstrates comparable accuracy to and is markedly faster than the state-of-the-art software. Moreover, CellFishing.jl is scalable to more than one million cells, and the throughput of the search is approximately 1600 cells per second.
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