Integrations & Recipes#
This section is for practical “how do I get my data out of this object?” workflows.
cellucid-r intentionally has minimal dependencies, so it does not accept Seurat/SCE objects directly.
Instead, you extract:
embeddings (UMAP 2D/3D)
a latent space (often PCA)
obs(cell metadata)optional gene expression + gene metadata
optional connectivities / vector fields
Then you call cellucid_prepare().
If you want the deep API docs (shapes, dtypes, file formats), see Data Preparation API.
Seurat Recipe
End-to-end export from a Seurat object (UMAP + PCA + metadata + expression + optional SNN graph).
SingleCellExperiment Recipe
End-to-end export from an SCE object (reducedDims + colData + assays).
Raw Matrices + Data Frames
Minimal-dependency workflow: just matrices/data.frames, no Seurat/SCE required.