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

Author:
Sato, Kenta, Tsuyuzaki, Koki, Shimizu, Kentaro, Nikaido, Itoshi
Source:
Genome biology 2019 v.20 no.1 pp. 31
ISSN:
1474-760X
Subject:
computer software, data collection, genes, sequence analysis, transcriptome
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.
Agid:
6306329