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CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA-sequencing

Kenta Sato, Koki Tsuyuzaki, Kentaro Shimizu, Itoshi Nikaido
doi: https://doi.org/10.1101/374462
Kenta Sato
1Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, 113-8657, Tokyo, Japan
2Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research, Wako, 351-0198, Saitama, Japan
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  • For correspondence: bicycle1885@gmail.com
Koki Tsuyuzaki
2Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research, Wako, 351-0198, Saitama, Japan
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Kentaro Shimizu
1Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, 113-8657, Tokyo, Japan
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Itoshi Nikaido
2Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research, Wako, 351-0198, Saitama, Japan
3Bioinformatics Course, Master’s/Doctoral Program in Life Science Innovation (T-LSI), School of Integrative and Global Majors (SIGMA), University of Tsukuba, Wako, 351-0198, Saitama, Japan
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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).

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Posted July 25, 2018.
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CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA-sequencing
Kenta Sato, Koki Tsuyuzaki, Kentaro Shimizu, Itoshi Nikaido
bioRxiv 374462; doi: https://doi.org/10.1101/374462
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CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA-sequencing
Kenta Sato, Koki Tsuyuzaki, Kentaro Shimizu, Itoshi Nikaido
bioRxiv 374462; doi: https://doi.org/10.1101/374462

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