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Acceleration of Large-Scale Single Cell Differential Gene Expression Analysis with FastDE

Connolly, E.; Aluru, M.; Chocklingam, S.; Dhere, V.; Gibson, G.; Pan, T.

2023-06-16 bioinformatics
10.1101/2023.06.15.545003 bioRxiv
Show abstract

The major bottleneck in single cell transcriptomic processing is identification of marker genes for individual cell clusters. We introduce FastDE, an implementation of the standard Wilcoxon Rank Sum test in C++ that results in 50X speed-up of the standard Seurat pipeline on a dataset of 1.2 million cells. Proof of methodology is demonstrated by replicating age and gender effects on immune cell differentiation in two large PBMC atlases.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.