Benchmark datasets for Spotless

<p>In <strong>standards.tar.gz</strong>, the silver standards are formatted as silver_standard_<strong>i</strong>-<strong>j</strong>, where&nbsp;<strong>i&nbsp;</strong>refers to the originating single-cell dataset and j refers to the <em>synthspot</em> abundance pattern. Each directory of the silver standard contains 10 replicates. All reference datasets are in the 'reference/' folder.</p> <p><strong>Single-cell dataset:</strong></p> <ol> <li>Brain cortex</li> <li>Single-cell cerebellum</li> <li>Single-nucleus cerebellum</li> <li>Hippocampus</li> <li>Kidney</li> <li>Squamous cell carcinoma</li> <li>Melanoma</li> </ol> <p><strong>Abundance patterns:</strong></p> <ol> <li>Uniform distinct</li> <li>Diverse distinct</li> <li>Uniform overlap</li> <li>Diverse overlap</li> <li>Dominant cell type</li> <li>Partially dominant cell type</li> <li>Rare cell type</li> <li>Regionally rare cell type</li> <li>Missing cell types</li> </ol> <p>We only uploaded .rds files to keep the file size smaller. For more information on file conversion, please visit the GitHub repository.</p> <p>To use&nbsp;<strong>liver_dataset.tar.gz, </strong>please read liver_README.txt before proceeding.</p> <p><strong>dataset_visualizations.zip</strong> contain visualizations of the gold standard, silver standard, and case study datasets.</p> <p><strong>raw_results.zip </strong>contains the proportions and evaluation metrics of each method, as well as aggregated metrics used to generate plots. They can be used in tandem with the <a href="https://github.com/saeyslab/spotless-benchmark/tree/main/scripts" target="_blank" rel="noopener">scripts</a> in the GitHub repository.</p>