{"doi":"10.1093/bioadv/vbaf314","title":"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+ implements a generic optimal transport solution that can be reduced to multiple different previously studied OT optimization procedures including SCOT, SCOTv2, SCOOTR, and AGW for single cell, each of which provides state-of-the-art single-cell alignment performance. Outside of giving a unified framework to interact with prior formulations, the generality of SCOT+ optimization naturally gives rise to a new OT loss, Unbalanced Augmented Gromov-Wasserstein (UAGW), and a corresponding optimizer. 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. Availability and implementation: Our 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/).","journal":"Bioinformatics Advances","year":2025,"id":584460,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9433,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1119243,"name":"Tuan Minh Pham","orcid":"0000-0003-2869-0165","position":1,"is_corresponding":false},{"id":550840,"name":"Pınar Demetçi","orcid":"0000-0002-5644-0326","position":2,"is_corresponding":false},{"id":1458047,"name":"Quang Huy Tran","orcid":"0000-0001-7771-3154","position":3,"is_corresponding":false},{"id":988323,"name":"Ievgen Redko","orcid":"0000-0002-3860-5502","position":4,"is_corresponding":false},{"id":550842,"name":"Björn Sandstede","orcid":"0000-0002-5432-1235","position":5,"is_corresponding":false},{"id":347248,"name":"Ritambhara Singh","orcid":"0000-0002-7523-160X","position":6,"is_corresponding":false},{"id":1458501,"name":"Colin Baker","orcid":null,"position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-19T02:59:11.978098Z","pmid":"42180428","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}