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Fig. 1 | Genome Biology

Fig. 1

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

Fig. 1

Schematic workflow of CellFishing.jl. CellFishing.jl first builds a database (DB) object that stores data preprocessors, indexed bit vectors, and cell metadata, if provided. The metadata can store any information including cell names, cell types, and transcript expressions of marker genes. When building a database, the DGE matrix of reference cells is preprocessed to extract important signals and then hashed into bit vectors by LSH. The preprocessors and the indexed bit vectors are stored in the database object. M, D, and T on the left side of the figure refer to the number of genes, number of reduced dimensions, and length of the bit vectors, respectively. N and N above the two DGE matrices represent the number of cells within the reference and query data, respectively. While searching the database for similar cells, the prebuilt preprocessors stored in the database are reused in a similar workflow that is involved in database building up to the hashing phase. The database object can be saved onto a disk and can be loaded from there

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