R Package Guide#
This guide documents the cellucid R package (repo: cellucid-r): how to export single-cell data from R into the Cellucid viewer export format so you can explore it in the Cellucid web app.
Note
cellucid-r is an export-focused package. It does not embed the viewer in R yet (no RStudio widget / Shiny integration yet).
If you want notebook embedding, servers, and programmatic control, see the Python Package Guide docs instead.
For the web UI experience after export (loading, filtering, analysis, sessions, community annotation), see Web App Guide.
Where to start (pick one)#
“I have a Seurat object” → Seurat Recipe
“I have a SingleCellExperiment” → SingleCellExperiment Recipe
“I just have matrices/data.frames” → Raw Matrices + Data Frames (Minimal Dependencies)
“I want to understand what gets written to disk” → What Is an Export Folder?
“I want to export vector fields (velocity/drift overlays)” → Vector Fields (Velocity / Displacement)
“I want a full end-to-end walkthrough” → Notebook Tutorials
“Something failed” → Troubleshooting Index
Chapters (what each folder contains)#
Quick starts and “what is this?” explanations for mixed audiences.
How R exports map to the browser viewer, plus dataset identity and reproducibility.
Deep documentation of cellucid_prepare() / prepare() including shapes, dtypes, edge cases, and file outputs.
How to open exported folders in the Cellucid web app, and how to host them for sharing.
Practical recipes for Seurat and SingleCellExperiment (and “raw matrix” workflows).
Very detailed, notebook-style walkthroughs with lots of “why”, edge cases, and troubleshooting.
A map of what parts of the R API are documented where (useful for maintainers and contributors).
Implementation notes, testing/release guidance, and codebase architecture for cellucid-r contributors.
Symptom → diagnosis → fix across installation, exports, and web app loading.