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How to Streamline RNA-Seq analysis and increase productivity—point, click, and done
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t-SNE produces a t-SNE task node. Opening the task report launches a scatter plot showing the t-SNE results. The plot will open in 2D or 3D depending on the user preference.
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Basic t-SNE parameters
Split cells by sample
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t-SNE preserves the local structure of the data by focusing on the distances between each point and its nearest neighbors. Perplexity can be thought of as the number of nearest neighbors being considered. The optimal perplexity depends on the size and density of the data. Generally, a larger and/or more dense data set will benefit from a higher perplexity (Figure 12). Default is 30. The range of possible values is 3 to 100.
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