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CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing
- Sato, Kenta, Tsuyuzaki, Koki, Shimizu, Kentaro, Nikaido, Itoshi
- Genome biology 2019 v.20 no.1 pp. 31
- computer software, data collection, genes, sequence analysis, transcriptome
- 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.