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It constructs a condition-specific domain-adaptive network founded on variational autoencoders. scDisco not only effectively reduces batch effects but also successfully disentangles biological effects and condition-specific effects, and further augmenting condition-specific representations through the utilization of condition-specific Domain-Specific Batch Normalization layers. This enhancement enables the identification of genes specific to particular conditions. The effectiveness and robustness of scDisco as an integration method were analyzed using both simulated and real datasets, and the results demonstrate that scDisco can yield high-quality visualizations and quantitative outcomes. Furthermore, scDisco has been validated using real datasets, affirming its proficiency in cell clustering quality, retaining batch-specific cell types and identifying condition-specific genes.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>scDisco is an effective integration method based on variational autoencoders, which improves analytical tasks of reducing batch effects, cell clustering, retaining batch-specific cell types and identifying condition-specific genes.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-024-05706-9","type":"journal-article","created":{"date-parts":[[2024,3,16]],"date-time":"2024-03-16T15:01:36Z","timestamp":1710601296000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Integration of scRNA-seq data by disentangled representation learning with condition domain adaptation"],"prefix":"10.1186","volume":"25","author":[{"given":"Renjing","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kun","family":"Qian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinwei","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongwei","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,3,16]]},"reference":[{"issue":"1","key":"5706_CR1","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1038\/nri.2017.76","volume":"18","author":"E Papalexi","year":"2018","unstructured":"Papalexi E, Satija R. 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