Individual skill
umap-tsne-analysis
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.
awesome-med-research-skills/Data Analysis/umap-tsne-analysis/SKILL.md
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- bioinformatics Repository topic
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# UMAP and t-SNE Analysis
## Prerequisites
Run the following before the first analysis to install all required R packages:
```bash
Rscript scripts/install_dependencies.R
```
Alternative manual installation:
```bash
Rscript -e "install.packages(c('optparse','data.table','Rtsne','umap','ggplot2','vegan','R.utils'), repos='https://cloud.r-project.org')"