fastEmbedR: native UMAP and t-SNE workflows
Overview | Select the backend and CPU core count | A first analysis | A bundled Bioconductor expression dataset | Parameter philosophy and intended scope | Choosing between UMAP and t-SNE | Optional downstream graph clustering | PCA and reproducible t-SNE initialization | Reusing a nearest-neighbor graph | Independent UMAP initialization | UMAP graph modes | Float32 and memory-conscious analysis | Embedding new observations | Landmarking | Measuring embedding quality | CPU, Metal, and CUDA | Package boundary | UMAP implementation | Interpolation-based t-SNE implementation | Graph clustering and landmarking | Backend reporting and software acknowledgements | A practical analysis checklist | References