Installation#

Audience: everyone
Time: 5–15 minutes (depending on your setup)

Requirements#

  • R: cellucid currently targets R ≥ 4.3.0.

  • Hard dependency: jsonlite

  • Optional but recommended: Matrix (sparse matrices + connectivities)

Note

cellucid-r is designed to be dependency-light and does not require Seurat or SingleCellExperiment. Those packages are only needed if you want to follow the Seurat/SCE recipes in this guide.

Verify the installation#

library(cellucid)
packageVersion("cellucid")

You should see:

  • No error on library(cellucid)

  • A version like 0.9.0 (or similar) from packageVersion

Troubleshooting installation#

Symptom: “package ‘jsonlite’ is not available”#

Likely causes

  • You are using an R environment without CRAN configured.

  • You are offline or behind a restrictive proxy.

How to confirm

  • Run getOption("repos") and verify you have a CRAN mirror set.

Fix

options(repos = c(CRAN = "https://cloud.r-project.org"))
install.packages("jsonlite")

Symptom: GitHub install fails (“HTTP error 401/403”, “rate limit”)#

Likely causes

  • Corporate proxy / blocked GitHub

  • GitHub API rate limiting

Fix options

  • Try pak (often more resilient).

  • If needed, configure a GitHub PAT:

    • Sys.setenv(GITHUB_PAT = "...")

Symptom: “there is no package called ‘Matrix’”#

Fix

install.packages("Matrix")

Symptom: you installed but library(cellucid) loads the wrong version#

How to confirm

find.package("cellucid")
packageVersion("cellucid")

Fix

  • Restart R (RStudio: Session → Restart R).

  • Reinstall with:

    remotes::install_github("theislab/cellucid-r", force = TRUE)

Next steps#