CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing
Kenta Sato, Koki Tsuyuzaki, Kentaro Shimizu, Itoshi Nikaido
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.
- :Genome Biology
- : 10.1186/s13059-019-1639-x
- : https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1639-x