Iterative single-cell multi-omic integration using online learning
| العنوان: | Iterative single-cell multi-omic integration using online learning |
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| المؤلفون: | April R Kriebel, Joshua D. Welch, Chao Gao, Sebastian Preissl, Joseph R. Ecker, Angeline Rivkin, Rosa Castanon, Justin P. Sandoval, Bing Ren, M. Margarita Behrens, Jialin Liu, Joseph R. Nery, Chongyuan Luo |
| المصدر: | Nature Biotechnology. 39:1000-1007 |
| بيانات النشر: | Springer Science and Business Media LLC, 2021. |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | 0303 health sciences, business.product_category, business.industry, Computer science, Online learning, Biomedical Engineering, Bioengineering, Single copy, computer.software_genre, Applied Microbiology and Biotechnology, Matrix decomposition, 03 medical and health sciences, Arbitrarily large, 0302 clinical medicine, Laptop, Scalability, Molecular Medicine, The Internet, Data mining, business, computer, 030217 neurology & neurosurgery, Reference dataset, 030304 developmental biology, Biotechnology |
| الوصف: | Integrating large single-cell gene expression, chromatin accessibility and DNA methylation datasets requires general and scalable computational approaches. Here we describe online integrative non-negative matrix factorization (iNMF), an algorithm for integrating large, diverse and continually arriving single-cell datasets. Our approach scales to arbitrarily large numbers of cells using fixed memory, iteratively incorporates new datasets as they are generated and allows many users to simultaneously analyze a single copy of a large dataset by streaming it over the internet. Iterative data addition can also be used to map new data to a reference dataset. Comparisons with previous methods indicate that the improvements in efficiency do not sacrifice dataset alignment and cluster preservation performance. We demonstrate the effectiveness of online iNMF by integrating more than 1 million cells on a standard laptop, integrating large single-cell RNA sequencing and spatial transcriptomic datasets, and iteratively constructing a single-cell multi-omic atlas of the mouse motor cortex. |
| تدمد: | 1546-1696 1087-0156 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_________::2804762e06021b3116650e1dc71d8790 https://doi.org/10.1038/s41587-021-00867-x |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi...........2804762e06021b3116650e1dc71d8790 |
| قاعدة البيانات: | OpenAIRE |
Find this article in full text from Springer Verlag. | تدمد: | 15461696 10870156 |
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