SCOT+: A Comprehensive Software Suite for Single-Cell alignment Using Optimal Transport
Abstract
Summary
New 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 Availability
Our algorithm is implemented in Pytorch and available on PyPI and GitHub (<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/scotplus/scotplus">https://github.com/scotplus/scotplus</ext-link>). Additionally, we have many tutorials available in a separate GitHub repository (<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/scotplus/book_source">https://github.com/scotplus/book_source</ext-link>) and on our website (<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://scotplus.github.io/">https://scotplus.github.io/</ext-link>).
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