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ArchMap: A web-based platform for reference-based analysis of single-cell datasets

Lotfollahi, M.; Bright, C.; Skorobogat, R.; Dehkordi, M.; George, X.; Richter, S.; Topalova, A.; Luecken, M. D.; Theis, F. J.

2024-09-19 bioinformatics
10.1101/2024.09.19.613883 bioRxiv
Show abstract

Leveraging single cell reference atlases to analyse new data has brought about a paradigm shift in single cell data science akin to the first reference genome in genomics. However methods to perform this mapping require computational expertise as well as sometimes considerable compute power, and thus may exclude the researchers from this innovation who may benefit the most from it. ArchMap, a no-code query-to-reference mapping tool, removes this barrier by providing all-in-one automated mapping, cell type annotation, and collaborative features to analyse single-cell datasets from a wide range of integrated, often published, reference atlases and allows extension of atlases with the growing Human Cell Atlas and related efforts. This paves the way for a democratisation of reference mapping capabilities.

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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.