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bioRxiv · 10.1101/2025.05.21.655322

SCOT+: A Comprehensive Software Suite for Single-Cell alignment Using Optimal Transport

Baker, C. D.·Pham, T. M.·Demetci, P.·Tran, Q.-H.·Redko, I.·Sandstede, B.·Singh, R.
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Abstract

SummaryNew advances in single-cell multi-omics experiments have allowed biologists to examine how various biological factors regulate processes in concert on the cellular level. However, measuring multiple cellular features for a single cell can be quite resource-intensive or impossible with the current technology. By using optimal transport (OT) to align cells and features across disparate datasets produced by separate assays, Single Cell alignment using Optimal Transport+ (SCOT+), our unsupervised single-cell alignment software suite, allows biologists to align their data without the need for any correspondence. SCOT+ has a generic optimal transport solution that can be reduced to multiple different OT optimization procedures, each of which provide state-of-the-art single-cell alignment performance. With our user-friendly website and tutorials, this new package will help improve biological analyses by allowing for more accurate downstream analyses on multi-omics single-cell measurements. Implementation and AvailabilityOur algorithm is implemented in Pytorch and available on PyPI and GitHub (https://github.com/scotplus/scotplus). Additionally, we have many tutorials available in a separate GitHub repository (https://github.com/scotplus/book_source) and on our website (https://scotplus.github.io/).

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Baker, C. D., Pham, T. M., Demetci, P., Tran, Q.-H., Redko, I., Sandstede, B., Singh, R.. 2025-05-27. SCOT+: A Comprehensive Software Suite for Single-Cell alignment Using Optimal Transport. https://doi.org/10.1101/2025.05.21.655322

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