CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA-sequencing
CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA-sequencing
Abstract Recent technical improvements in single-cell RNA sequencing (scRNA-seq) have enabled massively parallel profiling of transcriptomes, thereby promiting 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 data sets for similar cells with high accuracy and throughput. Using multiple scRNA-seq data sets, 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 1,350 cells per second (i.e., 0.74 ms per cell).
Tsuyuzaki Koki、Shimizu Kentaro、Nikaido Itoshi、Sato Kenta
Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics ResearchDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of TokyoLaboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research||Bioinformatics Course, Master?ˉs/Doctoral Program in Life Science Innovation (T-LSI), School of Integrative and Global Majors (SIGMA), University of TsukubaDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo||Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research
生物科学研究方法、生物科学研究技术计算技术、计算机技术分子生物学
scRNA-seqCell searchingCell typingLocality-sensitive hashing
Tsuyuzaki Koki,Shimizu Kentaro,Nikaido Itoshi,Sato Kenta.CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA-sequencing[EB/OL].(2025-03-28)[2025-04-28].https://www.biorxiv.org/content/10.1101/374462.点此复制
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