RT Journal Article
SR Electronic
T1 CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA-sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 374462
DO 10.1101/374462
A1 Sato, Kenta
A1 Tsuyuzaki, Koki
A1 Shimizu, Kentaro
A1 Nikaido, Itoshi
YR 2018
UL http://biorxiv.org/content/early/2018/07/25/374462.abstract
AB 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).