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It operates by optimizing a combination of multiple objectives using a Frank-Wolfe algorithm to produce a high quality transfer. Apart from transferring cell types/states to spatial omics, `DOT` can be used for transferring other relevant categorical or continuous features from one set of omics to another, such as estimating the expression of missinng genes or transferring transcription factor/pathway activities.\n\n\n\u003cp align=\"center\" width=\"100%\"\u003e\n  \u003cimg src=\"man/figures/overview.png\" align=\"center\" width=\"65%\"\u003e\n\u003c/p\u003e\n    \nFor more information about how this package has been used with real data and expected outputs, please check the following link:\n    \n- [DOT's general usage](https://saezlab.github.io/DOT/articles/general.html)\n\n## Installation\n`DOT` is available under the R package `DOTr` which you can install from [GitHub](https://github.com/) with:\n\n```r\ndevtools::install_github(\"saezlab/DOT\")\n```\n\n## Dependencies\n\n-   R (\u003e= 4.0)\n-   R packages: fields, ggplot2, Matrix, methods, Seurat, stats, stringr\n\nFor optimal performance on moderately sized instances, we recommend at least 4 GB of RAM. For large reference scRNA-seq data or very large spatial instances higher memory may be required.\n\nInstallation takes less than five minutes. The sample dataset provided can be run in less than a minute on a \"normal\" desktop computer. DOT takes approximately 7 minutes to process a MERFISH MOp dataset with approximately 250 genes, 100 cell types and 4,000 spots.\n\nOperating system tested on: macOS Monterey 12.4\n\n## Citation\nIf you use **DOT** for your research please cite the [following article](https://doi.org/10.1038/s41467-024-48868-z): \n\n\u003e Rahimi, A., Vale-Silva, L.A., Fälth Savitski, M. et al. DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics. Nat Commun 15, 4994 (2024). https://doi.org/10.1038/s41467-024-48868-z.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fdot","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fdot","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fdot/lists"}