Cellucid (R)

Export single-cell data from R to Cellucid — interactive, GPU-accelerated visualization in the browser.

cellucid (repo: cellucid-r) writes your embeddings, metadata, gene expression, connectivities, and vector fields to the on-disk format consumed by the Cellucid web app.

Highlights

• Exporter-only: generate a shareable “export folder” and open it in the web app
• Minimal dependencies: hard dependency jsonlite (optional/recommended: Matrix)
• Flexible inputs: works with raw matrices/data.frames, with docs recipes for Seurat and SingleCellExperiment
• Optional extras: gene expression, connectivity graphs, and vector fields for overlays like velocity/drift

Installation

Install from GitHub:

install.packages("remotes")
remotes::install_github("theislab/cellucid-r")

Optional but recommended (sparse matrices + connectivity export):

install.packages("Matrix")

Quickstart

library(cellucid)

cellucid_prepare(
  latent_space = latent,   # cells × dims
  obs = obs,               # data.frame (cells × fields)
  var = var,               # data.frame (genes × fields)
  gene_expression = expr,  # optional: cells × genes
  X_umap_2d = umap2,       # optional
  out_dir = "exports/my_dataset",
  force = TRUE
)

Links

• Web app
• Documentation
• Recipes: Seurat · SingleCellExperiment
• Source: cellucid-r · cellucid
• Citation: citation("cellucid")

Community

• Contributing: CONTRIBUTING.md
• Code of Conduct: CODE_OF_CONDUCT.md
• Security: SECURITY.md
• Support: SUPPORT.md
• GitHub citation metadata: CITATION.cff

License

BSD-3-Clause