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umap-tsne-analysis

separate

Use when performing sample-level dimensionality reduction and visualization on abundance or OTU-style matrices with a companion group file, generating UMAP and/or t-SNE coordinates and plots for group separation assessment. NOT for: differential expression testing, single-cell workflows requiring dedicated embeddings pipelines, or analyses without a sample grouping file.

When to use

• sample-level dimensionality reduction
• visualization on abundance or OTU-style matrices
• generating UMAP coordinates
• generating t-SNE coordinates
• group separation assessment

When not to use

• differential expression testing
• single-cell workflows requiring dedicated embeddings pipelines
• analyses without a sample grouping file

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